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Subject: Biology And Life Sciences, Biophysics Keywords: viral particles; radiobiology; RNA detection; microbiology; matter identification; particle physics; physical modelling; particle accelerators in environmental studies

Online: 10 May 2021 (15:35:15 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201909.0273.v2

Disentangling the Amyloid Pathways: A Mechanistic Approach to Etiology

Maja Malmberg, Tarja Malm, Oskar Gustafsson, Anthony Wright, Samir El Andaloussi, Anders Linden, Kariem Ezzat

Subject: Biology And Life Sciences, Biophysics Keywords: amyloid; virus; nucleation; loss-of-function; Alzheimer's; Parkinson's; prion; protein-only

Online: 19 November 2019 (03:53:09 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202004.0126.v1

Cold Atmospheric Plasma for COVID-19

Zhitong Chen, Richard Wirz

Subject: Biology And Life Sciences, Biophysics Keywords: Cold atmospheric Plasma; sterilization; Plasma-activated medium; Nitric oxide; Immunotherapy; COVID-19

Online: 8 April 2020 (11:34:11 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202104.0606.v1

Role of alpha-Synuclein in Cell Biology: A Hypothesis

Renu Minda

Subject: Biology And Life Sciences, Biophysics Keywords: Parkinson disease; alpha-synuclein; thermodynamics; Carnot cycle; mitochondria

Online: 22 April 2021 (10:47:07 CEST)

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Preprint HYPOTHESIS | doi:10.3390/sci1020054

Are Scientific Models of Life Testable? A Lesson from Simpson’s Paradox

Prasanta S. Bandyopadhyay, Nolan Grunska, Don Dcruz, Mark C. Greenwood

Subject: Biology And Life Sciences, Biophysics Keywords: emergence of life; game of life; inefficiency objection; simpson’s paradox; astrobiology

Online: 16 September 2019 (00:00:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0194.v1

AGTR2, One Possible Novel Key Gene for the Entry of 2019-nCoV into Human Cells

Qinghua Cui, Chunmei Cui, Chuanbo Huang, Wanlu Zhou, Xiangwen Ji, Fenghong Zhang, Liang Wang, Yuan Zhou

Subject: Biology And Life Sciences, Biophysics Keywords: 2019-nCoV; receptor; ACE2; AGTR2

Online: 14 February 2020 (10:52:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints201907.0090.v1

Surface Tension and Viscosity of Blood

Adam Wesołowski, Anna Młynarczak

Subject: Biology And Life Sciences, Biophysics Keywords: surface tension; viscosity; blood

Online: 5 July 2019 (05:08:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201608.0114.v1

Assessment of in Vivo Oxidative Stress Biomarkers in Relation to Disease Progression and Cell Proliferation in Benign and Malignant Breast Diseases

Kanchan Karki, Deepti Pande, Reena Negi, Ranjana Khanna, H D Khanna

Subject: Biology And Life Sciences, Biophysics Keywords: 8-OHdG (8-hydroxy- 2-deoxyguanosine), vitamin A, vitamin C, vitamin E, ROS (reactive oxygen species), TAS (total antioxidant status)

Online: 10 August 2016 (16:49:20 CEST)

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Preprint ARTICLE | doi:10.3390/sci1030058

Thermodynamic Jump from Prebiotic Microsystems to Primary Living Cells

Vladimir Kompanichenko

Subject: Biology And Life Sciences, Biophysics Keywords: origin of life; prebiotic system; living cell; oscillation; organic molecule; experiment; hydrothermal system

Online: 6 October 2019 (00:00:00 CEST)

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Preprint CASE REPORT | doi:10.3390/sci1030060

Assessment of Static Steadiness and Dynamic Stability at Various Stages of Healing a Grade 2 Medial Collateral Ligament Tear

Kaycee Glattke, Michael Smith, Toshiki Tsuchiya, Jakob Wells, Thurmon Lockhart

Subject: Biology And Life Sciences, Biophysics Keywords: biomechanics; dynamic stability; inertial measurement unit; MCL tear; static stability

Online: 15 October 2019 (00:00:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201611.0015.v1

Transmural Cellular Heterogeneity in Myocardial Electromechanics

Anastasia Khokhlova, Nathalie Vikulova, Leonid Katsnelson, Gentaro Iribe, Olga Solovyova

Subject: Biology And Life Sciences, Biophysics Keywords: cardiac transmural heterogeneity; electromechanical coupling; mechano-calcium-electric feedback; cardiac modeling; cardiomyocyte

Online: 2 November 2016 (06:58:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints201904.0325.v1

A Complete Biological Theory of Sleep

Ari Rappoport

Subject: Biology And Life Sciences, Biophysics Keywords: sleep; anesthesia; rapid eye movement (REM) sleep; NREM sleep; sharp-wave ripples (SWRs); dreaming; consciousness

Online: 30 April 2019 (11:12:47 CEST)

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Preprint ARTICLE | doi:10.3390/sci1020053

Organic Molecules: Is It Possible to Distinguish Aromatics from Aliphatics Collected by Space Missions in High Speed Impacts?

Mark Burchell, Kathryn Harriss

Subject: Biology And Life Sciences, Biophysics Keywords: astrobiology; enceladus; space-missions; organic; aromatic; aliphatic

Online: 13 September 2019 (00:00:00 CEST)

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A prime site of astrobiological interest within the Solar System is the interior ocean of Enceladus. This ocean has already been shown to contain organic molecules and is thought to have the conditions necessary for more complex organic biomolecules to emerge and potentially even life itself. This sub-surface ocean has been accessed by Cassini, an unmanned spacecraft that interacted with the water plumes ejected naturally from Enceladus. The encounter speed with these plumes and their contents was 5 km s⁻¹ and above. Encounters at such speeds allow analysis of vaporised material from submicron-sized particles within the plume, but sampling micron-sized particles remains an open question. The latter particles can impact metal targets exposed on the exterior of future spacecraft, producing impact craters lined with impactor residue, which can then be analysed. Although there is considerable literature on how mineral grains behave in such high-speed impacts, and also on the relationship between the crater residue and the original grain composition, far less is known regarding the behaviour of organic particles. Here we consider a deceptively simple yet fundamental scientific question: for impacts at speeds of around 5–6 kms⁻¹ would the impactor residue alone be sufficient to enable us to recognise the signature conferred by organic particles? Furthermore, would it be possible to identify the organic molecules involved, or at least distinguish between aromatic and aliphatic chemical structures? For polystyrene (aromatic-rich) and poly (methyl methacrylate) (solely aliphatic) latex particles impinging at around 5 km s⁻¹ onto metal targets, we found that sufficient residue is retained at the impact site to permit identification of a carbon-rich projectile, but not of the particular molecules involved, nor is it currently possible to discriminate between aromatic-rich and solely aliphatic particles. This suggests that an alternative analytical method to simple impacts on metal targets is required to enable successful collection of organic samples in a fly-by Enceladus mission.

Preprint REVIEW | doi:10.20944/preprints202004.0510.v1

A Structural View at SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping

Maria Romano, Alessia Ruggiero, Flavia Squeglia, Giovanni Maga, Rita Berisio

Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV-2; COVID19; RNA replication; protein structure; infectious disease

Online: 29 April 2020 (12:52:18 CEST)

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Preprint REVIEW | doi:10.20944/preprints202005.0518.v1

From Extracellular Vesicles to Global Environment: A Cosmopolite SARS-Cov-2 Virus

Veronika Kralj-Iglič, Raja Dahmane, Tjaša Griessler Bulc, Polonca Trebše, Saba Battelino, Mojca Bavcon Kralj, Metka Benčina, Klemen Bohinc, Darja Božič, Mojca Debeljak, Drago Dolinar, Aleš Iglič, Darja Istenič, Zala Jan, Monika Jenko, Marko Jeran, Gregor Jereb, Mojca Jevšnik, Aleksandra Krivograd Klemenčič, Tomaž Lampe, Irina Milisav, Andreea Oarga-Mulec, Andrej Ovca, Borut Poljšak, Franja Prosenc, Anna Romolo, Nina Resnik, Robert Sotler, Anja Šoštarič, Vid Šuštar, Urška Šunta, Urška Štibler, Bojana Uršič, Domen Vozel

Subject: Biology And Life Sciences, Biophysics Keywords: virus; extracellular vesicles; COVID-19; SARS-CoV-2; membrane vesicluation

Online: 31 May 2020 (21:35:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0393.v1

Virtual Screening and Molecular Dynamics Simulation Suggest Valproic Acid Co-A could Bind to SARS-CoV2 RNA Depended RNA Polymerase

Neel Sarovar Bhavesh, Anupam Patra

Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV2; RNA depended RNA polymerase; Valproic acid Co-A; drug repurposing

Online: 26 March 2020 (15:04:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints201904.0232.v1

A Machine Learning Approach for the Discovery of Ligand-specific Functional Mechanisms of GPCRs

Ambrose Plante, Derek M. Shore, Giulia Morra, George Khelashvili, Harel Weinstein

Subject: Biology And Life Sciences, Biophysics Keywords: functional selectivity; biased ligands; molecular dynamics; deep neural networks; sensitivity analysis; pharmacological efficacy

Online: 22 April 2019 (10:54:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0439.v1

Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site

Umesh Kalathiya, Monikaben Padariya, Marcos Mayordomo, Małgorzata Lisowska, Judith Nicholson, Ashita Singh, Maciej Baginski, Robin Fåhraeus, Neil Carragher, Kathryn Ball, Juergen Haas, Alison Daniels, Ted R. Hupp, Javier Antonio Alfaro

Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV-2; COVID-19; spike glycoprotein; variability; molecular docking; molecular dynamics; inhibitors

Online: 24 April 2020 (11:42:01 CEST)

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Preprint REVIEW | doi:10.20944/preprints201705.0129.v1

Phenotypic Plasticity and Cell Fate Decisions in Cancer: Insights from Dynamical Systems Theory

Dongya Jia, Mohit Kumar Jolly, Prakash Kulkarni, Herbert Levine

Subject: Biology And Life Sciences, Biophysics Keywords: cell fate decision; cancer attractors; gene network dynamics; EMT; drug resistance; intrinsically disordered proteins

Online: 17 May 2017 (06:25:17 CEST)

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Waddington’s epigenetic landscape, a famous metaphor in developmental biology, depicts how a stem cell progresses from an undifferentiated phenotype to a differentiated one. The concept of “landscape” in the context of dynamical system theory represents a high-dimensional cell state space, in which each cell phenotype is considered as an “attractor” that is determined by interactions among multiple variables (molecular players), and is buffered against environmental fluctuations. Further, biological noise is thought to play an important role during these cell-fate decisions and in fact controls transitions between different phenotypes. Here, we discuss these phenotypic transitions in cancer from a dynamical systems perspective and invoke the concept of “cancer attractors” – hidden stable states of the underlying regulatory network that are not occupied by normal cells. Using epithelial-to-mesenchymal transition (EMT), cancer stem-like properties, metabolic reprogramming and the emergence of drug/hormone resistance as examples, we illustrate how phenotypic plasticity in cancer cells enables them to acquire hybrid phenotypes (such as hybrid epithelial/mesenchymal and hybrid metabolic phenotypes) that tend to be more aggressive and notoriously resilient to drug/hormone treatment. Furthermore, we highlight multiple factors that may give rise to phenotypic plasticity in cancer cells, such as (a) multi-stability or oscillatory behaviors governed by underlying regulatory networks involved in cell-fate decisions in cancer cells, and (b) network rewiring due to conformational dynamics of intrinsically disordered proteins (IDPs) that are highly enriched in cancer cells. We conclude by discussing why a therapeutic approach that promotes ‘recanalization’, i.e. the exit from “cancer attractors” and re-entry into “normal attractors”, is more likely to succeed rather than a conventional approach that targets individual molecules/pathways.

Preprint REVIEW | doi:10.20944/preprints201908.0271.v1

Insights from Molecular Dynamics Simulations for GPCR Drug Discovery

Ye Zou, John Ewalt, Ho-Leung Ng

Subject: Biology And Life Sciences, Biophysics Keywords: GPCRs; membrane protein; molecular dynamics; protein structure; drug design; biased-signaling pathway; allosteric sites

Online: 26 August 2019 (15:34:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201902.0122.v1

Leishmania Proteomics: An in Silico Perspective

Carlos A. Padilla, Maria J. Alvarez, Aldo Combariza

Subject: Biology And Life Sciences, Biophysics Keywords: computational

Online: 13 February 2019 (15:44:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints201703.0133.v1

Sunburn Protection by Sunscreen Sprays at Beach

Hao Ou-Yang, Richard Bradley Rzendzian

Subject: Biology And Life Sciences, Biophysics Keywords: erythema; swimming; re-application; exposed skin surface; natural sunlight

Online: 17 March 2017 (04:59:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints201708.0065.v1

4SM Method Tested in the Gulf of California Suggests Field Data are Not Needed to Derive Satellite Bathymetry

Fabio Favoretto, Yann Morel, Andrew Waddington, Jorge Lopez-Calderon, Marco Cadena-Roa, Anidia Blanco-Jarvio

Subject: Biology And Life Sciences, Biophysics Keywords: 4SM; satellite derived bathymetry; water depth; water column correction; remote sensing; Landsat; San Lorenzo Channel

Online: 18 August 2017 (12:14:16 CEST)

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Preprint REVIEW | doi:10.20944/preprints201803.0043.v1

Orientating the Future Bio-Macromolecular Electron Microscopy

Fei Sun

Subject: Biology And Life Sciences, Biophysics Keywords: cryo-electron microscopy; air-water interface; conformational heterogeneity; focus gradient; radiation damage

Online: 6 March 2018 (07:17:15 CET)

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Preprint REVIEW | doi:10.20944/preprints201909.0241.v1

Mechanotransduction in Neuronal Cell Development and Functioning

Matteo Chighizola, Tania Dini, Cristina Lenardi, Paolo Milani, Alessandro Podestà, Carsten Schulte

Subject: Biology And Life Sciences, Biophysics Keywords: mechanobiology; biophysics; neuronal differentiation; biomaterials; bioengineering

Online: 20 September 2019 (18:59:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201802.0138.v1

Structural and Functional Characterization of RNA-binding Site of Rev and Rev-Response-Element RNA Complex via All Atom Molecular Dynamics Simulations

Zaheer Ul-Haq, Nizakat Ali, Mohamed H. Al-Agamy, Assem Barakat

Subject: Biology And Life Sciences, Biophysics Keywords: molecular dynamics simulation; RNA-binding; rev protein; rev response element (RRE); HIV-virus.

Online: 21 February 2018 (16:57:27 CET)

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Nuclear export of viral mRNAs, is an essential step in the HIV replication cycle. This role is played by a small regulatory protein of HIV-1 called Rev.The N-terminal region of Rev contains an arginine-rich sequence. The arginine-rich motif (ARM) is located between amino acids 38-50 and forms an alpha-helical secondary structure. Expression of the structural proteins of human immunodeficiency virus type 1 requires the direct interaction of multiple copies of the viral Rev protein with its highly structured RNA target sequence, the Rev Response element (RRE). The major viral proteins are not produced if this transport of RNA is stopped. Therefore, knowledge of Rev structure is essential for understanding of its cooperative binding to the RRE, for understanding the mechanism of HIV infection and for the development of antiviral drugs that interfere with Rev’s essential functions and for acknowledgment of good candidate drugs for treatment of AIDS. To understand how REV interact with RRE element of HIV-RNA and its formation of oligomeric complex it is better to characterize the domain wise structure of REV with regard in function of each domain. Due to lack of structural data on Rev no single compound is reported as inhibitor of REV expect antiviral drugs. Identification of a high-affinity RNA-binding site for the human immunodeficiency virus type 1 Rev Protein is much more important. The ARM is a highly specific sequence which allows for the multimerization of Rev and also binding of REV with RNA. Here we are first time exploring the structural characteristics of REV protein both in free form and in complex with RNA at domain function level especially explore the role of ARM motif in REV HIV-1 protein as RNA binding sites by molecular dynamics (MD) simulation and homology modeling studies. Results indicate that the arginine-rich motif (ARM) is crucial in stability of this complex. The residues ARG38, 39, 41, 43, 44, 48, 50, and ASN40 are most interacting with nucleobases of RRE in Crystal structure of Rev and Rev-response-element RNA complex. Our study plays a major role in elaboration of binding of RNA with REV and pave the way for further investigation for therapeutically agent for HIV.

Preprint ARTICLE | doi:10.20944/preprints201809.0569.v1

Chemotherapeutic Drug Functionalized Nanoparticles are Beneficial When Treating Breast Cancer Via Magnetic Hyperthermia

Susann Piehler, Heidi Dähring, Julia Grandke, Julia Göring, Pierre Couleaud, Antonio Aires, Aitziber L. Cortajarena, José Courty, Alfonso Latorre, Álvaro Somoza, Rodolfo Miranda, Ingrid Hilger

Subject: Biology And Life Sciences, Biophysics Keywords: magnetic hyperthermia, magnetic nanoparticles (MNP), doxorubicin (DOX), NucAnt (N6L), breast cancer, mouse model

Online: 28 September 2018 (13:29:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201803.0071.v1

S-layer Protein-based Biosensors

Bernhard Schuster

Subject: Biology And Life Sciences, Biophysics Keywords: biosensor; S-layer protein; crystalline 2D protein lattice; lipid membrane platform; linking matrix; bioreceptor; biomimetics

Online: 9 March 2018 (12:10:28 CET)

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Preprint REVIEW | doi:10.20944/preprints201812.0273.v2

Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases

Yunhui Peng, Emil Alexov, Sankar Basu

Subject: Biology And Life Sciences, Biophysics Keywords: mutations; disease-causing mutations; polymorphism; folding free energy change; binding free energy change; drug discovery; in silico screening

Online: 23 January 2019 (09:10:48 CET)

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Preprint REVIEW | doi:10.20944/preprints201805.0413.v1

A Current Overview of the Molecular Effects of Nanosilver

Shana J. Cameron, William G. Willmore

Subject: Biology And Life Sciences, Biophysics Keywords: silver nanoparticles; nanosilver; endocytosis; oxidative stress; reactive oxygen species; inflammation; wound healing; hypoxia; mitochondria; endoplasmic reticulum stress; unfolded protein response; autophagy; apoptosis; angiogenesis; epigenetics; genotoxicity; cancer; anti-cancer

Online: 28 May 2018 (15:51:12 CEST)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints202203.0146.v1

Expansion Microscopy on Saccharomyces cerevisiae

Artemis G. Korovesi, Leonor Morgado, Marco Fumasoni, Ricardo Henriques, Hannah Heil, Mario Del Rosario

Subject: Biology And Life Sciences, Biophysics Keywords: expansion microscopy; yeast; Saccharomyces cerevisiae; super-resolution

Online: 10 March 2022 (10:51:02 CET)

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Preprint ARTICLE | doi:10.20944/preprints201909.0273.v1

Disentangling the Amyloid Pathways: A Mechanistic Approach to Etiology

Maja Malmberg, Tarja Malm, Oskar Gustafsson, Anthony Wright, Samir El Andaloussi, Anders Linden, Kariem Ezzat

Subject: Biology And Life Sciences, Biophysics Keywords: amyloid; virus; nucleation; loss-of-function; Alzheimer's; Parkinson's; prion

Online: 24 September 2019 (12:13:12 CEST)

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Preprint REVIEW | doi:10.20944/preprints201807.0059.v1

Data Normalization in NMR-based Metabolomics

Helena Zacharias, Michael Altenbuchinger, Wolfram Gronwald

Subject: Biology And Life Sciences, Biophysics Keywords: data normalization; data scaling; zero-sum; metabolic fingerprinting; NMR; statistical data analysis

Online: 3 July 2018 (16:22:31 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints201906.0278.v1

Structural Changes in the Acceptor Site of Photosystem II Upon Ca2+/Sr2+ Exchange in the Mn4CaO5 Cluster Site and the Possible Long-Range Interactions

Faisal Hammad Mekky Koua

Subject: Biology And Life Sciences, Biophysics Keywords: photosystem II; redox potential; electron transfer; charge separation; photo-inhibition

Online: 27 June 2019 (05:54:13 CEST)

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Preprint REVIEW | doi:10.20944/preprints201807.0016.v3

Advances and Challenges of Biodegradable Implant Materials with a Focus on Magnesium-Alloys and Bacterial Infections

Muhammad Imran Rahim, Sami Ullah, Peter P. Mueller

Subject: Biology And Life Sciences, Biophysics Keywords: bioresorbable implants; corrosion layer; vascular stents; orthopedic implants; microbial infections

Online: 11 July 2018 (13:54:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201807.0231.v1

Measurements of Dynamic Contributions to Coherent Neutron Scattering

Sebastian Jaksch, Alexandros Koutsioubas, Stefan Mattauch, Olaf Holderer, Henrich Frielinghaus

Subject: Biology And Life Sciences, Biophysics Keywords: phospholipids; membranes; GISANS; GINSES; coherent scattering; spectroscopy

Online: 13 July 2018 (10:51:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201902.0122.v2

Leishmania Proteomics: An in Silico Perspective

Carlos A. Padilla, Maria J. Alvarez, Aldo F. Combariza

Subject: Biology And Life Sciences, Biophysics Keywords: computational chemistry; biophysics; proteomics

Online: 24 May 2019 (12:49:58 CEST)

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Preprint REVIEW | doi:10.20944/preprints202305.0503.v1

Emerging Quantitative Biochemical, Structural and Biophysical Methods to Study Ribosome and Protein-RNA Complex Assembly

Kavan Gor, Olivier Duss

Subject: Biology And Life Sciences, Biophysics Keywords: RNP assembly; ribosome assembly; protein-RNA interactions; RNA folding; assembly intermediates; in vitro reconstitutions; mass spectrometry; single-molecule fluorescence microscopy; cryo-electron microscopy; RNA structure probing

Online: 8 May 2023 (10:01:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0018.v1

The Aggregation Conditions Define Whether EGCG Is an Inhibitor or Enhancer of α-Synuclein Amyloid Fibril Formation

Rebecca Sternke-Hoffmann, Alessia Peduzzo, Najoua Bolakhrif, Rainer Haas, Alexander K. Buell

Subject: Biology And Life Sciences, Biophysics Keywords: amyloid; α-synuclein; EGCG; inhibition

Online: 3 February 2020 (05:45:33 CET)

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Preprint REVIEW | doi:10.20944/preprints201812.0273.v3

Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases

Yunhui Peng, Emil Alexov, Sankar Basu

Subject: Biology And Life Sciences, Biophysics Keywords: mutations; disease-causing mutations; polymorphism; folding free energy change; binding free energy change; drug discovery; in silico screening

Online: 28 January 2019 (11:39:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints201804.0284.v1

Insight into the Self-Assembling Properties of a Peptergent: A Molecular Dynamics Study

Jean-Marc Crowet, Mehmet Nail Nasir, Antoine Deschamps, Vincent Stroobant, Pierre Morsomme, Magali Deleu, Patrice Soumillion, Laurence Lins

Subject: Biology And Life Sciences, Biophysics Keywords: peptide; self-assembly; molecular dynamics; peptergency; beta structure

Online: 23 April 2018 (11:27:51 CEST)

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Preprint REVIEW | doi:10.20944/preprints202007.0034.v1

Proton Transfer Mechanisms in Bimetallic Hydrogenases

Hulin Tai, Shun Hirota, Sven T. Stripp

Subject: Biology And Life Sciences, Biophysics Keywords: hydrogen; biocatalysis; hydride chemistry; photochemistry; infrared spectroscopy

Online: 3 July 2020 (12:12:12 CEST)

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Hydrogenases are iron-sulfur enzymes that catalyze proton reduction and H₂ oxidation with outstanding efficiency. They are considered blueprints for the design of transition metal complexes, e.g. as heterogenous catalysts in the context of H₂ production from water. Moreover, hydrogenases are biological model systems for metal hydride chemistry and proton-coupled electron transfer. Depending on the composition of the active site cofactor, [NiFe]-hydrogenases are distinguished from [FeFe]-hydrogenases. The former binds a hetero bimetallic nickel/iron site, embedded in the protein by four cysteine ligands. The later, by contrast, carries a homo bimetallic iron/iron site attached to the protein by only a single cysteine. Carbon monoxide and cyanide ligands (CO/CN) at the active site facilitated detailed investigations of hydrogenase catalysis by infrared spectroscopy, owing to strong signals and redox-dependent frequency shifts. However, the details of proton transfer have not been addressed experimentally.We found that specific redox state transitions in [NiFe]- and [FeFe]-hydrogenase can be triggered by visible light to record extremely sensitive ‘light-minus-dark’ infrared difference spectra monitoring key amino acid residues as shown in the ToC figure. As these transitions are coupled to protonation changes, our data allowed investigating dynamic hydrogen-bonding changes that go well beyond the resolution of protein crystallography. In [NiFe]-hydrogenase, photolysis of the bridging hydride ligand in the ‘Ni-C’ state was followed by rapid accumulation of the ‘Ni-SI_a’ state and/or ‘Ni-L’ state. Infrared difference spectra in various isotopic media clearly indicated the formation of a protonated cysteine residue as well as hydrogen-bonding changes involving the COOH group of a glutamic acid residue and a ‘dangling water’ molecule. These findings are in excellent agreement with crystallographic analyses of [NiFe]-hydrogenase in the Ni-R state and allowed devising a molecular precise model of catalytic proton transfer. In [FeFe]-hydrogenase, an external redox dye was used to accumulate the ‘Hred’ state over the oxidized resting state ‘Hox’. Infrared difference spectra of wild-type enzyme and numerous amino acid variants indicated hydrogen-bonding changes involving the COOH groups of two glutamic acid residues. Moreover, we noted the deprotonation of an arginine residue. Crystallographic analyses of [FeFe]-hydrogenase in the Hox state failed to explain the rapid proton transfer due to a ‘breach’ in the succession of residues. To this end, our findings facilitated a molecular precise model of ‘discontinued’ proton transfer.The comparison of catalytic proton transfer in bimetallic hydrogenases emphasizes the role of the outer coordination sphere. We suggest that the stable protonation of a nickel-ligating cysteine in [NiFe]-hydrogenase has a crucial influence on the preferred direction of proton flow and catalysis (i.e., H₂ oxidation). On the contrary, proton transfer in [FeFe]-hydrogenase involves an adjacent cysteine as a relay group that promotes both proton release and proton uptake. We presume that this causes the notable bidirectionality of [FeFe]-hydrogenase. These observations must guide the design of biomimetic compounds for the production or consumption of H₂.

Preprint REVIEW | doi:10.20944/preprints201807.0008.v1

Membrane Active Peptides and Their Biophysical Characterization

Fatma Gizem Avci, Berna Sariyar Akbulut, Elif Ozkirimli

Subject: Biology And Life Sciences, Biophysics Keywords: antimicrobial peptides; cell-penetrating peptides; biophysical characterization; uptake mechanism; membrane disruption; peptide-lipid interactions

Online: 2 July 2018 (10:37:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0570.v1

Towards the Unification of Quantum Dynamics, Relativity and Living Organisms

Arturo Tozzi, James F. Peters, John S. Torday

Subject: Biology And Life Sciences, Biophysics Keywords: Einstein; manifold; Hilbert space; Abelian; living cell; Borsuk-Ulam theorem; topology

Online: 28 September 2018 (13:32:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0369.v1

Temperature Extreme May Exaggerate the Mortality Risk of COVID-19 in the Low- and Middle-income Countries: A Global Analysis

Mizanur Rahman, Mahmuda Islam, Mehedi Hasan Shimanto, Jannatul Ferdous, Abdullah Al-Nur Shanto Rahman, Pabitra Singha Sagor, Tahasina Chowdhury

Subject: Biology And Life Sciences, Biophysics Keywords: temperature extreme; warm climate; low-and middle-income economies; COVID-19; mortality; mixed effect modelling

Online: 30 June 2020 (11:38:15 CEST)

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Preprint REVIEW | doi:10.20944/preprints201912.0245.v1

Are Microbes Thermodynamically Optimised Self-Reproducing Machines?

Nima P. Saadat, Tim Nies, Yvan Rousset, Oliver Ebenhöh

Subject: Biology And Life Sciences, Biophysics Keywords: energy; entropy; anabolism; catabolism; microbial cultures; biotechnology

Online: 19 December 2019 (07:00:02 CET)

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To understand microbial growth with mathematical models has a long tradition that dates back to the pioneering work of Jacques Monod in the 1940s. Growth laws are simple mathematical expressions that aim at describing growth rates of microbes as functions of external parameters, in particular nutrient concentrations. These laws are now widely applied to construct, e.g., dynamic ecosystem models. However, to explain the growth laws from underlying (first) principles is extremely challenging. In the second half of the 20th century, numerous experimental approaches aimed at precisely measuring heat production during microbial growth to determine the entropy balance in a growing cell and to quantify the exported entropy. This has led to the development of thermodynamic theories of microbial growth, which have generated fundamental understanding and identified principle limitations of the growth process. Whereas these approaches considered a growing microbe as a black box, modern theories heavily rely on genomic resources to describe and model genome-scale networks to explain microbial growth. Interestingly, however, thermodynamic constraints are often included in modern modelling approaches only in a rather superficial fashion, and it appears that recent modelling approaches and classical theories are disconnected fields. In order to stimulate a closer interaction between these fields, we here review various theoretical approaches that aim at describing microbial growth based on thermodynamic principles. We start with classical black-box models of cellular growth, and continue with genome-scale modelling approaches that include thermodynamics, before we place these models in the context of fundamental considerations based on non-equilibrium statistical mechanics. We conclude by identifying conceptual overlaps between the fields and suggest how the various types of theories and models can be integrated. We outline how concepts from one approach may help to inform or constrain another, and we demonstrate how genome-scale models can be used to infer classical black-box parameters, which are experimentally accessible in growth experiments. Such integration will allow understanding to what extent microbes can be viewed as thermodynamic machines, and how close they operate to theoretical optima.

Preprint REVIEW | doi:10.20944/preprints201903.0095.v1

Insights into Actin-Myosin Interactions within Muscle from 3-D Electron Microscopy

Kenneth A. Taylor, Hamidreza Ramani, Robert J. Edwards, Michael K. Reedy

Subject: Biology And Life Sciences, Biophysics Keywords: Striated Muscle, image reconstruction, muscle physiology

Online: 7 March 2019 (12:42:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202207.0120.v1

Using Brains as Sensors of the Magnetic Fields Produced by Other Brains

Énora Jeuland, Matthieu Lenne, Florence Jarry, Jacques Bruno Debruille

Subject: Biology And Life Sciences, Biophysics Keywords: Brain; sensitivity to EMFs; EEG; ERPs; N400; LPP; joint processing effects (JPEs)

Online: 7 July 2022 (09:19:44 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202003.0459.v1

Are Qualia Reducible, Physical Entities?

Christian Matthias Kerskens

Subject: Biology And Life Sciences, Biophysics Keywords: topological quantum brain; quantum computing; Majorana Zero modes; qualia; consciousness

Online: 31 March 2020 (10:41:35 CEST)

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Preprint REVIEW | doi:10.20944/preprints201904.0206.v1

Quantifying Cancer Epithelial-Mesenchymal Plasticity and Its Association with Stemness and Immune Response

Dongya Jia, Xuefei Li, Federico Bocci, Shubham Tripathi, Youyuan Deng, Mohit Kumar Jolly, José N. Onuchic, Herbert Levine

Subject: Biology And Life Sciences, Biophysics Keywords: helial-mesenchymal transition; EMT spectrum; hybrid epithelial/mesenchymal phenotypes; CTC clusters; stemness; immune suppression; EMT metrics; systems biology

Online: 18 April 2019 (08:02:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201904.0292.v1

Structuredness as a Measure of the Complexity of the Structure and the Role of Post-Dissipative Structures and Ratchet Processes in Evolution

George Mikhailovsky

Subject: Biology And Life Sciences, Biophysics Keywords: complexity; information; entropy; structuredness measure; dissipative and post-dissipative structures; structuregenesis; evolution

Online: 26 April 2019 (09:42:39 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202104.0606.v2

Role of a-Synuclein in Cell Biology: A Hypothesis and its Implications in Neurodegenerative Diseases

Renu Minda

Subject: Biology And Life Sciences, Biophysics Keywords: Parkinson’s disease; alpha-synuclein; Lewy bodies; phase transition; thermodynamics; and mitochondria

Online: 10 January 2022 (12:23:19 CET)

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Preprint SHORT NOTE | doi:10.20944/preprints202005.0017.v1

Life and Evolution in Terms of Maximum Entropy Production Principle

Leonid Martyushev

Subject: Biology And Life Sciences, Biophysics Keywords: definition of life; evolution; entropy production; MEPP

Online: 2 May 2020 (15:54:19 CEST)

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Preprint REVIEW | doi:10.20944/preprints201809.0236.v1

Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques—Searching for Mechanism and Kinetics of Biomolecular Functions

Hiroshi Fujisaki, Kei Moritsugu, Yasuhiro Matsunaga

Subject: Biology And Life Sciences, Biophysics Keywords: molecular dynamics simulation; rare event; string method; multiscale enhanced sampling; weighted ensemble; multidrug transporter; Onsager-Machlup action

Online: 13 September 2018 (12:01:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0265.v1

p53 Transactivation Domain Mediates Binding and Phase Separation With poly-PR/GR

Sinem Usluer, Emil Spreitzer, Benjamin Bourgeois, Tobias Madl

Subject: Biology And Life Sciences, Biophysics Keywords: poly-PR/GR; neurodegenerative disease; LLPS; p53; intrinsically disordered domains; membraneless organelles

Online: 15 September 2021 (14:43:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0390.v1

COVID-19 Diagnosis by 5-second Facial Video Processing Using Vibraimage and Artificial Intelligence

Viktor Minkin, Valery Akimov

Subject: Biology And Life Sciences, Biophysics Keywords: COVID-19; vibraimage; behavioral parameters; diagnosis accuracy; ANN; AI

Online: 22 September 2021 (16:28:12 CEST)

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The Covid-19 pandemic spreads in waves for a year and a half, despite significant worldwide efforts, the development of biochemical diagnostic methods and population vaccination. One of the reasons for the infection spread is the impossibility of early disease detection through biochemical diagnostics, since biochemical processes slowly develop in a body. At the same time, well known that behavioral characteristics of a person, measured based on reflex movements, are capable for inertialess assessment of psychophysiological parameters. Vibraimage technology is the method of head micromovements video processing by inter-frame difference accumulation and converting spatial and temporal characteristics of the inter-frame difference into behavioral and psychophysiological parameters. Here we shown that behavioral parameters measured by vibraimage changed during COVID-19 infection. The identification of changes signs in behavioral parameters detected by AI trained on patients and controls. The best diagnostic accuracy (higher 94%) obtained using instantaneous values of behavioral parameters measured with the following vibraimage settings: 10Hz frequency of basic measurements; 25 inter-frame difference accumulations and averaging the diagnostic results over period of at least 5 seconds. COVID-19 diagnoses by behavioral parameters showed earlier (5-7 days) detection of the disease compared to symptoms and positive results of biochemical RT-PCR testing. Proposed method for COVID-19 diagnosis indicates infected persons within 5 seconds video processing using standard television cameras (web, IP) and computers, allows mass testing/selftesting and will stop the pandemic spread. We assume that head micromovements analysis for diagnosis of various diseases is possible not only with the help of vibraimage technology. Further research of human head micromovement analysis will help stop the COVID-19 pandemic and will contribute to the development of new contactless and environmentally friendly methods for early diagnosis of diseases.

Preprint REVIEW | doi:10.20944/preprints202108.0453.v1

Biophysical and Biochemical Attributes of Hybrid Epithelial/Mesenchymal Phenotypes

Subbalakshmi Ayalur Raghu, Bazella Ashraf, Mohit Kumar Jolly

Subject: Biology And Life Sciences, Biophysics Keywords: Hybrid epithelial/mesenchymal phenotypes; Collective cell migration; epithelial-mesenchymal heterogeneity; mathematical modeling; cell-state transition; live-cell imaging

Online: 23 August 2021 (14:32:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201903.0147.v1

Myosin Cross-bridge Behaviour in Contracting Muscle – The T₁ Curve of Huxley & Simmons (1971) Revisited

Carlo Knupp, John M. Squire

Subject: Biology And Life Sciences, Biophysics Keywords: myosin filament stiffness; actin filament stiffness; myosin cross-bridge stiffness; muscle transients; weak binding heads; contractile mechanism; cross-bridge cycle; rigor muscle

Online: 14 March 2019 (07:01:45 CET)

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The stiffness of the myosin cross-bridges is a key factor in analysing possible scenarios to explain myosin head changes during force generation in active muscles. The seminal study of Huxley and Simmons (1971: Nature 233: 533) suggested that most of the observed half-sarcomere instantaneous compliance (=1/stiffness) resides in the myosin heads. They showed with a so-called T₁ plot that, after a very fast release, the half-sarcomere tension reduced to zero after a step size of about 60Å (later with improved experiments reduced to 40Å). However, later X-ray diffraction studies showed that myosin and actin filaments themselves stretch slightly under tension, which means that most (at least two-thirds) of the half sarcomere compliance comes from the filaments and not from cross-bridges. Here we have used a different approach, namely to model the compliances in a virtual half sarcomere structure in silico. We confirm that the T₁ curve comes almost entirely from length changes in the myosin and actin filaments, because the calculated cross-bridge stiffness (probably greater than 0.4 pN/Å) is higher than previous studies have suggested. In the light of this, we present a plausible modified scenario to describe aspects of the myosin cross-bridge cycle in active muscle. In particular, we suggest that, apart from the filament compliances, most of the cross-bridge contribution to the instantaneous T₁ response comes from weakly-bound myosin heads, not myosin heads in strongly attached states. The strongly attached heads would still contribute to the T₁ curve, but only in a very minor way, with a stiffness that we postulate could be around 0.1 pN/Å, a value which would generate a working stroke close to 100 Å from the hydrolysis of one ATP molecule. The new program can serve as a tool to calculate sarcomere elastic properties for any vertebrate striated muscle once various parameters have been determined (e.g. tension, T₁ intercept, temperature, X-ray diffraction spacing results).

Preprint ARTICLE | doi:10.20944/preprints202004.0297.v1

Gold Nanoparticle Mediated Multi-Modal CT Imaging of 3 Hsp70 Membrane Positive Tumors

Melanie A. Kimm, Maxim Shevtsov, Caroline Werner, Wolfgang Sievert, Zhiyuan Wu, Oliver Schoppe, Bjoern H. Menze, Ernst J. Rummeny, Roland Proksa, Olga Bystrova, Marina Martynova, Gabriele Multhoff, Stefan Stangl

Subject: Biology And Life Sciences, Biophysics Keywords: gold nanoparticle; heat shock protein 70; molecular imaging; biomarker; spectral-CT; k-edge imaging

Online: 17 April 2020 (08:42:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0284.v1

Identity, structure and compositional analysis of adjuvanted vaccines

Kristen Kalbfleisch, Moriam Ore, Sasmit Deshmukh, Wayne Williams, Ibrahim Durowoju, Jessica Duprez, Carmen Mei, Sylvie Morin, Joan Bevilacqua, Bruce Carpick, Marina Kirkitadze

Subject: Biology And Life Sciences, Biophysics Keywords: adsorbed vaccines, identity, protein conformation, particle sizing, FTIR, SEM, Fluorescence

Online: 16 August 2018 (12:54:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0582.v1

Can Semaglutide Bind Tighter to GLP-1R?

Wei Li

Subject: Biology And Life Sciences, Biophysics Keywords: Semaglutide; GLP-1R; Interfacial Biophysics

Online: 24 July 2020 (11:58:41 CEST)

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Working Paper ARTICLE

Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons

Enrique Maciá

Subject: Biology And Life Sciences, Biophysics Keywords: double-stranded DNA; DNA dynamical models; correlated oscillations in macromolecules; epigenetic changes

Online: 4 January 2021 (16:35:40 CET)

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Working Paper ARTICLE

Towards Understanding of Polymorphism of G-Rich Region of Human Papillomavirus Type 52

Maja Marušič, Janez Plavec

Subject: Biology And Life Sciences, Biophysics Keywords: G-quadruplex; NMR; folding; DNA; structure; human papillomaviruses

Online: 18 March 2019 (10:00:21 CET)

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Preprint REVIEW | doi:10.20944/preprints201912.0179.v1

Sheaves in the Brain Elucidate the Behavior of Entrained Oscillations

Arturo Tozzi

Subject: Biology And Life Sciences, Biophysics Keywords: globular set; category theory; multidimensional; visual recognition; drug-resistant epilepsy; transcranial magnetic stimulation.

Online: 13 December 2019 (10:37:03 CET)

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Preprint ARTICLE | doi:10.20944/preprints201909.0146.v1

Entropy Production as the Origin of Information Encoding in RNA and DNA

Julián Mejía, Karo Michaelian

Subject: Biology And Life Sciences, Biophysics Keywords: entropy; entropy production; non-equilibrium thermodynamics; information encoding; nucleic acids; DNA; RNA; origin of life; origin of codons; amino acids; stereochemical era; photon potential

Online: 14 September 2019 (19:44:54 CEST)

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Preprint REVIEW | doi:10.20944/preprints201803.0043.v2

Orientating the Future Bio-Macromolecular Electron Microscopy

Fei Sun

Subject: Biology And Life Sciences, Biophysics Keywords: cryo-electron microscopy; air-water interface; conformational heterogeneity; focus gradient; radiation damage

Online: 3 May 2018 (11:08:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202201.0022.v1

Potassium at the Origins of Life: Did Biology Emerge From Biotite in Micaceous Clay?

Helen Greenwood Hansma

Subject: Biology And Life Sciences, Biophysics Keywords: clay; mica; biotite; muscovite; origin of life; abiogenesis; mechanical energy; work; wet-dry cycles

Online: 4 January 2022 (20:36:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints201906.0290.v1

Intake of Molecular Hydrogen in Drinking Water Increases Membrane Transporters, p-Glycoprotein, and Multidrug resistance-associated Protein 2 without Affecting Xenobiotic-metabolizing Enzymes in Rat Liver

Hsien-Tsung Yao, Yu-Hsuan Yang, Mei-Ling Li

Subject: Biology And Life Sciences, Biophysics Keywords: molecular hydrogen; hydrogen-rich water; xenobiotic-metabolizing enzymes; membrane transporters; liver; oxidative stress

Online: 28 June 2019 (07:36:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0711.v1

The Interplay of Order and Disorder in the Dynamical Evolution of Physical and Biological Systems

Asima Tripathy, Rajat Kumar Pradhan

Subject: Biology And Life Sciences, Biophysics Keywords: order; entropy; chaos; evolution; cosmic mind; big bang

Online: 30 October 2018 (07:50:20 CET)

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Preprint ARTICLE | doi:10.20944/preprints201902.0240.v1

Visualizing Biological Membrane Organization and Dynamics

Marc Baaden

Subject: Biology And Life Sciences, Biophysics Keywords: Molecular visualization, Lipid bilayer

Online: 26 February 2019 (12:38:17 CET)

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Preprint REVIEW | doi:10.20944/preprints202103.0111.v1

Biophysics of Nervous Embryo-Fetal Development

Arturo Tozzi

Subject: Biology And Life Sciences, Biophysics Keywords: soft matter; liquid crystals; braid group; anyon; brain; microcolumn

Online: 2 March 2021 (16:56:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints201810.0299.v1

Curvature Changes in Biological Dynamics

Arturo Tozzi

Subject: Biology And Life Sciences, Biophysics Keywords: lines; brain; topology; curvature; Dickinsonia; fMRI

Online: 15 October 2018 (10:36:18 CEST)

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Working Paper ARTICLE

Optimal Microbiome Networks: Macroecology and Criticality

Jie Li, Matteo Convertino

Subject: Biology And Life Sciences, Biophysics Keywords: microbiome; complex networks; species diversity; criticality; RSA; information flow; transitions

Online: 28 March 2019 (09:10:18 CET)

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The human microbiome is an extremely complex ecosystem considering the amount of bacterial species, their interactions, and its variability over time. Here we untangle the complexity of the human microbiome for the Irritable Bowel Syndrome (IBS) that is the most prevalent functional gastrointestinal disorder in human populations. Based on a novel information theoretic network inference model we detect species interaction networks that are functionally and structurally different for healthy and unhealthy individuals. Healthy networks are characterized by a neutral symmetrical pattern of species interactions and scale-free topology versus random unhealthy networks. We detect an inverse scaling relationship between species total outgoing information flow, meaningful of node interactivity, and relative species abundance (RSA). The top ten interacting species are also the least relatively abundant for the healthy microbiome and the most detrimental. These findings support the idea about the diminishing role of network hubs and hubs should be defined considering the total outgoing information flow rather than the node degree. Macroecologically, the healthy microbiome is characterized by the highest total species diversity growth rate, the lowest species turnover, and the smallest variability of RSA for all species. This result challenges current views that posit a universal association between healthy states and the highest absolute species diversity in ecosystems. Additionally, we show how the transitory microbiome is unstable and microbiome criticality is not at the phase transition between healthy and unhealthy states. We stress out the importance of considering interacting pairs versus single node dynamics when characterizing the microbiome and of ranking these pairs in terms of their dynamics. Interactions (i.e. species collective behavior) shape transition from healthy to unhealthy states.\\ The macroecological characterization of the microbiome is useful for diagnostic purposes and disease etiognosis, while species-specific analyses can detect species that are more beneficial leading to personalized design of pre- and pro-biotic treatments and microbiome engineering.

Preprint ARTICLE | doi:10.20944/preprints201905.0031.v1

Variability and Reproducibility of Directed and Undirected Functional MRI Connectomes in the Human Brain

Allegra Conti, Andrea Duggento, Maria Guerrisi, Luca Passamonti, Iole Indovina, Nicola Toschi

Subject: Biology And Life Sciences, Biophysics Keywords: functional networks; functional magnetic resonance imaging; connectome; connectivity matrices; graphs; reproducibility; granger causality; transfer entropy

Online: 6 May 2019 (07:47:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202201.0046.v1

Veratridine Can Bind to a Site at the Mouth of the Channel Pore at Human Cardiac Sodium Channel NaV1.5

Alican Gulsevin, Andrew M Glazer, Tiffany Shields, Brett M Kroncke, Dan M Roden, Jens Meiler

Subject: Biology And Life Sciences, Biophysics Keywords: voltage-gated sodium channels; cardiac sodium channels; SCN5A; veratridine; toxins; molecular docking; Rosetta; electrophysiology; site-directed mutagenesis

Online: 5 January 2022 (18:02:52 CET)

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Preprint REVIEW | doi:10.20944/preprints201812.0193.v1

Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields

Maciej Pawel Ciemny, Aleksandra Elzbieta Badaczewska-Dawid, Monika Pikuzinska, Andrzej Kolinski, Sebastian Kmiecik

Subject: Biology And Life Sciences, Biophysics Keywords: coarse-grained; CABS model; MC simulations; statistical force fields; disordered protein; protein structure

Online: 17 December 2018 (10:54:32 CET)

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Preprint REVIEW | doi:10.20944/preprints201807.0016.v1

Advances and Challenges of Biodegradable Implant Materials with a Focus on Magnesium-Alloys and Bacterial Infections

Muhammad Imran Rahim, Sami Ullah, Peter P. Mueller

Subject: Biology And Life Sciences, Biophysics Keywords: bioresorbable implants; corrosion layer; vascular stents; orthopedic implants; microbial infections

Online: 2 July 2018 (16:34:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0008.v1

Symmetry Breaking and Emergence of Directional Flows in Minimal Actomyosin Cortices

Sven K. Vogel, Christian Wölfer, Diego A. Ramirez-Diaz, Robert J. Flassig, Kai Sundmacher, Petra Schwille

Subject: Biology And Life Sciences, Biophysics Keywords: bottom-up synthetic biology; motor proteins; pattern formation; self-organization

Online: 2 April 2020 (04:02:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202111.0098.v1

Multiscale Mapping of the Salt Marshes Using Sentinel-2, Dove and UAV Imagery in the Bay of Mont-Saint-Michel

Antoine Collin, Dorothée James, Antoine Mury, Mathilde Letard, Thomas Houet, Hélène Gloria, Eric Feunteun

Subject: Biology And Life Sciences, Biophysics Keywords: spatiotemporal analysis; high to ultra high spatial resolution; high to very high temporal resolution; NDVI; NIR; neural network modelling, Bay of Mont-Saint-Michel

Online: 4 November 2021 (09:35:50 CET)

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Preprint ARTICLE | doi:10.20944/preprints201905.0321.v1

Hox Gene Collinearity May Be Related to Noether’s Theory on Symmetry and Its Linked Conserved Quantities

Spyros Papageorgiou

Subject: Biology And Life Sciences, Biophysics Keywords: Hox genes, Hox collinearity, Noether’s Theory, Anterior Posterior axis, Rotational symmetry

Online: 27 May 2019 (14:14:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0368.v1

Infrared Characterization of the Bidirectional Oxygen-Sensitive [Nife]-Hydrogenase from E. Coli

Moritz Senger, Konstanin Laun, Basem Soboh, Sven Timo Stripp

Subject: Biology And Life Sciences, Biophysics Keywords: Metalloenzymes; Spectroscopy; Small Molecules

Online: 16 October 2018 (16:54:25 CEST)

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Preprint ESSAY | doi:10.20944/preprints201910.0354.v1

A Perceptive Scale Toolkit for Navigating Across Length Scales

Ipsa Jain, Minhaj Sirajuddin

Subject: Biology And Life Sciences, Biophysics Keywords: science communication; scale; education; toolkit

Online: 30 October 2019 (09:31:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints201905.0327.v1

Systematic Assessment of Freely-Diffusing Single-Molecule Fluorescence Detection using Brownian Motion Simulations

Dolev Hagai, Eitan Lerner

Subject: Biology And Life Sciences, Biophysics Keywords: single-molecule; fluorescence; burst; photon rate; effective detection volume; point-spread function; Brownian; diffusion; simulation; threshold.

Online: 28 May 2019 (10:13:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0050.v1

The Banach-Tarski Paradox Dictates Snyergistic Routes for Scale-Free Neurodynamics

Arturo Tozzi, James F. Peters

Subject: Biology And Life Sciences, Biophysics Keywords: Banach–Tarski paradox; brain; power law; fractal; oscillations; information

Online: 6 April 2020 (11:36:49 CEST)

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Preprint REVIEW | doi:10.20944/preprints201902.0122.v3

Leishmania Proteomics: An in Silico Perspective

Carlos A. Padilla, María J. Álvarez, Aldo F. Combariza

Subject: Biology And Life Sciences, Biophysics Keywords: Leishmania; leishmaniasis; Theoretical Physics and Chimistry; Molecular Dynamics

Online: 21 February 2020 (06:57:33 CET)

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Preprint REVIEW | doi:10.20944/preprints202204.0156.v1

Living Cell’s Feeling of Holes: The Mathematics of Cavities in Biophysical Structures

Arturo Tozzi

Subject: Biology And Life Sciences, Biophysics Keywords: nanovesicles; flow; homology; vortex; Betti number; Borsuk–Ulam theorem

Online: 18 April 2022 (06:14:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0248.v1

Early Critical Phase Transitions of Pericentromere-Associated Domains in MCF-7 Breast Cancer Cells Committed to Differentiation by Heregulin

Jekabs Krigerts, Kristine Salmina, Talivaldis Freivalds, Felikss Rumnieks, Inna Inashkina, Pawel Zayakin, Michael Hausmann, Jekaterina Erenpreisa

Subject: Biology And Life Sciences, Biophysics Keywords: cancer; differentiation commitment; acridine-orange-DNA test; pericentromere-associated domains (PADs); power law of PAD number vs. size; critical self-organisation; unravelling of PADs; silencing threshold

Online: 15 May 2020 (08:01:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0228.v1

Use of the Catastrophe Model to Preliminarily Explore the Principles of Multicellular Organization

Zheming Cao, Weidong Ding, Jun Qiang, Meiyao Wang, Haojun Zhu

Subject: Biology And Life Sciences, Biophysics Keywords: catastrophe model; multicellular organization; IPS cell

Online: 16 June 2022 (03:51:39 CEST)

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Thermodynamic studies consider living entities as dissipative structures. Organisms maintain and develop an orderly structure by exchanging matter, energy, and entropy with the surrounding environment; thus, maintaining life and growth. For a single cell, the temperature, volume, content concentration, and content complexity are four control variables. For warm-blooded animals, both temperature and content concentration are assumed to be constant, and only volume and content complexity, i.e., various proteins, nucleic acids, and small molecular substances in the cell and their interactions, are considered as acting variables. Thus, the potential function of a single cell should conform to the cusp catastrophe model. As the studies on the specific mathematical models of the relationship between the volume and content complexity are not available, we could not propose specific methods for the specific variants of the potential function of this cusp catastrophe model. We could only present our approximate results based on the basic characteristics of the cusp catastrophe model. We speculated that when a single cell is in a stable state, it cannot undergo differentiation, dedifferentiation, and division. These behaviors occur only when the cell enters an unstable state. Based on this speculation, we divided somatic cells of warm-blooded animals into two types, namely stable cells and non-steady cells. If we consider a warm-blooded animal as a whole dissipative structure, its control variables should have steady-state cells, non-steady-state cells, and negative entropy input. If we assume that the negative entropy input is constant, the proportion of non-steady cells and the total number of cells can be used as the control variables of the potential function. For warm-blooded animals, their potential function also conforms to the cusp catastrophe model. Because the studies on the relationship between the proportion of non-steady-state cells and the total cell number are rare, we could not propose specific methods for the variation of the potential function of this cusp catastrophe model. We could only present our approximate results according to the basic characteristics of the cusp catastrophe model. We speculated that as individuals, animals should be in a stable state during development. Once they enter an unstable state, they will fall ill or die. For humans, the proportion of non-steady cells decreases during the growth process from a fertilized egg to old age. From the fertilized egg to adulthood, the total cell number increases; however, in old age, the total cell number begins to decrease gradually. The entire developmental curve will gradually enter an unstable state. We speculated that once the developmental curve of a human enters an unstable state, it is death for the elderly.

Working Paper ARTICLE

On the Age-Specific Selection and the Emergence of Extensive Lifespan beyond Menopause

Tin Yau Pang

Subject: Biology And Life Sciences, Biophysics Keywords: ageing, menopause

Online: 9 May 2019 (11:42:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0101.v1

Insights in the Interaction of HPV-16 E6 and Its Variants (E-G350, E-A176/G350, E-C188/G350, AAa and AAc) with MAGI-1

Lilian Esmeralda Araujo- Arcos, Ciresthel Bello-Rios, Olga Lilia Garibay- Cerdenares, Marco Antonio Leyva-Vázquez, Sarita Montaño, Berenice Illades-Aguiar

Subject: Biology And Life Sciences, Biophysics Keywords: E6; variants; MAGI-1; molecular dynamic simulation; docking

Online: 6 September 2021 (13:51:17 CEST)

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Working Paper REVIEW

Physicochemical Foundations of Life that Direct Evolution. Why Chance and Natural Selection cannot Explain Evolution

Didier Auboeuf

Subject: Biology And Life Sciences, Biophysics Keywords: evolution; genetic code; RNA; protein; physicochemistry

Online: 28 November 2019 (09:38:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0106.v1

Characterization of Osteoarthritis in a Medial Meniscectomy-Induced Animal Model Using Contrast-Enhanced X-Ray Microtomography

Takehito Sugasawa, Tomoaki Kuji, Kai Aoki, Koki Yanazawa, Akiko Takenouchi, Makoto Watanabe, Yoshiya Tome, Yoshinori Takeuchi, Yuichi Aita, Naoya Yahagi, Yasuhiro Shishikura, Seikou Ono, Yasuko Yoshida, Yasushi Kawamai, Kazuhiro Takekoshi

Subject: Biology And Life Sciences, Biophysics Keywords: osteoarthritis; synovitis; articular cartilage; microfocus X-ray CT; 3D analysis

Online: 9 February 2020 (15:49:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints202102.0038.v1

Detection of Chymotrypsin by Optical and Acoustic Methods

Ivan Piovarci, Tibor Hianik, Ilia N. Ivanov

Subject: Biology And Life Sciences, Biophysics Keywords: chymotrypsin; β-casein; nanoparticles; UV-Vis spectroscopy; dynamic light scattering; quartz crystal microbalance.

Online: 1 February 2021 (13:59:40 CET)

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Working Paper ARTICLE

Endemics and Cosmopolitans: Application of Statistical Mechanics to the Dry Forests of Mexico

Michael G Bowler, Colleen K Kelly

Subject: Biology And Life Sciences, Biophysics Keywords: statistical mechanics; resource partitioning; distribution of species; seasonally dry tropical forest; biotic resistance

Online: 3 April 2019 (10:36:47 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202005.0423.v2

SARS-CoV-2 Virion Stabilization by Zn Binding

Silvia Morante, Giovanni La Penna, Giancarlo C. Rossi, Francesco Stellato

Subject: Biology And Life Sciences, Biophysics Keywords: Sars-CoV2; Zn Finger; orf7a/orf8 and Theterin

Online: 9 August 2020 (22:08:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0394.v1

Exploring patterns in modularity of protein interaction networks across the tree of life using Spectral Entropy

Anshuman Swain, Jesse Milzman, William F Fagan

Subject: Biology And Life Sciences, Biophysics Keywords: Modularity; Protein-to-protein interaction networks; Spectral characterization; Tree of life

Online: 17 May 2021 (16:56:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0234.v1

Physical Analysis of SARS-CoV-2 Routes: from Primary Production and Emissions to Exposures and COVID-19 Infection

Gjalt Huppes, Ruben Huele

Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV-2; COVID-19; virions mass balance; spatial modelling of toxics concentrations; human exposure to airborne substances; Substance Flow Analysis (SFA); environmental routes of toxic viruses; primary production of SARS-2 virions

Online: 17 May 2022 (14:19:43 CEST)

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Biology and Life Sciences