REVIEW | doi:10.20944/preprints201809.0236.v1
Subject: 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)
To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics are important to be characterized but its atomistic details are hard to obtain both experimentally and computationally. We review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: One is the Onsager-Machlup action method, and the other is the weighted ensemble method. Some applications of above methods to biomolecular systems are also discussed and illustrated.
REVIEW | doi:10.20944/preprints202106.0008.v1
Subject: Mathematics & Computer Science, Other Keywords: Multiscale modeling; Multiscale Systems; Megacities; Smart Cities; Multiscale Modeling Applications;
Online: 1 June 2021 (09:39:59 CEST)
Megacities are complex systems facing the challenges of overpopulation, poor urban design and planning, poor mobility and public transport, poor governance, climate change issues, poor sewerage and water infrastructure, waste and health issues, and unemployment. Smart cities have emerged to address these challenges by making the best use of space and resources for the benefit of citizens. A smart city model views the city as a complex adaptive system consisting of services, resources, and citizens that learn through interaction and change in both the spatial and temporal domains. The characteristics of dynamic development and complexity are key issues for city planners that require a new systematic and modeling approach. Multiscale modeling (MM) is an approach that can be used to better understand complex adaptive systems. The MM aims to solve complex problems at different scales, i.e., micro, meso, and macro, to improve system efficiency and mitigate computational complexity and cost. In this paper, we present an overview of MM in smart cities. First, this study discusses megacities, their current challenges, and their emergence to smart cities. Then, we discuss the need of MM in smart cities and its emerging applications. Finally, the study highlights current challenges and future directions related to MM in smart cities, which provide a roadmap for the optimized operation of smart city systems.
HYPOTHESIS | doi:10.20944/preprints202207.0106.v2
Subject: Life Sciences, Cell & Developmental Biology Keywords: mechanobiology; microgravity; macrophage; multiscale; MRTF; radiation
Online: 18 July 2022 (10:59:36 CEST)
Macrophages exhibit impaired phagocytosis, adhesion, migration, and cytokine production in space, hindering their ability to elicit immune responses. Considering that the combined effect of spaceflight microgravity and radiation is multiscale and multifactorial in nature, it is expected that contradictory findings are common in the field. This theory paper reanalyzes research on the macrophage spaceflight response across multiple timescales from seconds to weeks, and spatial scales from the molecular, intracellular, extracellular, to the physiological. Key findings include time-dependence of both pro-inflammatory activation and integrin expression. Here, we introduce the time-dependent, intracellular localization of MRTF-A as a hypothetical confounder of macrophage activation. We discuss the mechanosensitive MRTF-A/SRF pathway dependence on the actin cytoskeleton/nucleoskeleton, microtubules, membrane mechanoreceptors, hypoxia, oxidative stress, and intracellular/extracellular crosstalk. By adopting a multiscale perspective, this paper provides the first mechanistic answer for a three-decade-old question regarding impaired cytokine secretion in microgravity—and strengthens the connection between the recent advances in mechanobiology, microgravity, and the spaceflight immune response. Finally, we hypothesize MRTF involvement and complications in treating spaceflight-induced cardiovascular, skeletal, and immune disease.
CONCEPT PAPER | doi:10.20944/preprints202202.0094.v1
Subject: Engineering, Mechanical Engineering Keywords: turbulence; numerical simulation; multiscale modeling; stochastic processes
Online: 7 February 2022 (15:45:47 CET)
A multiscale modeling concept for numerical simulation of multiphysics turbulent flow utilizing map-based advection is described. The approach is outlined with emphasis on its theoretical foundations and physical interpretations in order to establish the context for subsequent presentation of the associated numerical algorithms and the results of validation studies. The model formulation is a synthesis of existing methods, modified and extended in order to obtain a qualitatively new capability. The salient feature of the approach is that time advancement of the flow is fully resolved both spatially and temporally, albeit with modeled advancement processes restricted to one spatial dimension. This one-dimensional advancement is the basis of a bottom-up modeling approach in which three-dimensional space is discretized into under-resolved mesh cells, each of which contains an instantiation of the modeled one-dimensional advancement. Filtering is done only to provide inputs to a pressure correction that enforces continuity and to obtain mesh-scale-filtered outputs if desired. The one-dimensional advancement, the pressure correction, and coupling of one-dimensional instantiations using a Lagrangian implementation of mesh-resolved volume fluxes is sufficient to advance the three-dimensional flow without time advancing coarse-grained equations, a feature that motivates the designation of the approach as autonomous microscale evolution (AME). In this sense, the one-dimensional treatment is not a closure because there are no unclosed terms to evaluate. However, the approach is additionally suitable for use as a subgrid-scale closure of existing large-eddy-simulation methods. The potential capabilities and limitations of both of these implementations of the approach are assessed conceptually and with reference to demonstrated capabilities of related methods.
ARTICLE | doi:10.20944/preprints202003.0083.v1
Subject: Materials Science, General Materials Science Keywords: multiscale simulation; fatigue; metals; CRSS; endurance limit
Online: 5 March 2020 (11:33:05 CET)
The paper introduces a valuable new description of fatigue strength in relation to material properties and thus a new perspective on the overall understanding of the fatigue process. Namely, a relation between the endurance limits and the accompanying values of the critical resolved shear stress (CRSS) for various metallic materials has been discovered by means of a multiscale approach for fatigue simulation. Based on the uniqueness of the relation, there is a strong indication that it is feasible to relate the endurance limit to the CRSS, and not to the ultimate strength as often done in the past.
REVIEW | doi:10.20944/preprints202202.0213.v1
Subject: Materials Science, Polymers & Plastics Keywords: Polymer nanocomposite; Multiscale modelling; Nanostructure; Nanoparticle; Interface; Simulation
Online: 17 February 2022 (11:51:28 CET)
This paper is focused on understanding multiscale modelling to obtain a bridge among different time and length scales of simulation techniques. These techniques are vital as it holds the potential to understand and predict the capabilities of polymer nanocomposites (PNCs). However, an appropriate approach in controlling the interfacial interaction between nanoparticle and polymer in nanocomposites structure is still needed to develop. In this review, an initial brief introduction to various trending simulation techniques has been discussed at all three levels of scale (nm, μm, mm). Later, descriptive study on fundamental issues such as thermodynamics, kinetics, mechanical properties, and morphology has been studied deeply. The multiscale modeling bridges the gaps of simulation between the different scales of models from molecular to mesoscale levels working over the broad range of length and timescale. Through the sequential, adaptive, and concurrent approaches, we can develop a system that may comprehend multiscale mode modeling adaptive resolution approach has recently added approach the molecule of the subject can shift their position freely in the domain and through this approach and studied the Brownian motion. Co-The co-current coach is also termed as handshaking path and it is linked aiming at different scale models. Covering the rigid techniques smoothly and linking them at different scales helps in normalizing the statistical behaviour.
ARTICLE | doi:10.20944/preprints202010.0322.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Multiscale orthonormal basis; High-order BVPs; Convergence order;
Online: 15 October 2020 (11:55:31 CEST)
This paper presents a numerical algorithm for solving high-order BVPs. We introduce the construction method of multiscale orthonormal basis in Wm[0; 1] by multiscale orthonormal basis in W1[0; 1]. We define approximate solution, and obtain the approximate solution of high-order BVPs by using the approximate theory. Moreover, the convergence and stability of the algorithm are improved. At last, several numerical experiments show the feasibility of the proposed method.
ARTICLE | doi:10.20944/preprints201905.0232.v1
Subject: Materials Science, Polymers & Plastics Keywords: modelling; carbon fiber composite; experimental mechanics; multiscale; defect
Online: 20 May 2019 (08:55:18 CEST)
A multiscale modelling approach was developed in order to estimate the effect of defects on the strength of unidirectional carbon fiber composites. The work encompasses a micromechanics approach, where the known reinforcement and matrix properties are experimentally verified and a 3D finite element model is meshed directly from micrographs. Boundary conditions for loading the micromechanical model are derived from macroscale finite element simulations of the component in question. Using a microscale model based on the actual microstructure, material parameters and load case allows realistic estimation of the effect of a defect. The modelling approach was tested with a unidirectional carbon fiber composite beam, from which the micromechanical model was created and experimentally validated. The effect of porosity was simulated using a resin-rich area in the microstructure and the results were compared to experimental work on samples containing pores.
Subject: Materials Science, General Materials Science Keywords: nanofiber; multiscale; X-ray tomography; composite filter media; numerical simulation
Online: 20 July 2020 (11:28:45 CEST)
Air filtration mechanisms in the composite filter media used in practical applications are important and challenging to understand because the component fibers could have various size scales and morphologies. In this work, a three-dimensional digital model of nanofiber-based filter media was reconstructed for the first time based on the X-ray tomography data for the cellulose substrate and the Focused Ion Beam-Scanning Electron Microscope (FIB-SEM) image analysis for the several microns thick (3.82-7.90 μm) electrospun polyvinylidene fluoride (PVDF) nanofiber membrane. Besides the high-resolution model where the details of the fibrous structures were fully resolved, another low-resolution model with approximated unresolved structures was also established. Filtration simulations utilizing these models were conducted considering the drag force, Brownian diffusion and aerodynamic slip. The simulated filtration efficiencies agreed well with the experiments for particles of 70-400 nm, including the most penetrating particle size (MPPS, 100-200 nm). Moreover, the structure-resolved models had higher accuracy but higher computational costs, while the unresolved simulations saved much running time but over-predicted the filtration efficiency, especially for smaller particles (<100 nm). Our study presents a comprehensive strategy for investigating the composite filter media with multiscale complex structures using a combination of advanced characterization technologies and modular simulation models.
REVIEW | doi:10.20944/preprints202007.0022.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Multiscale modelling; cell-based modelling; computational biology; multicellular systems biology
Online: 3 July 2020 (08:43:36 CEST)
The growth and dynamics of multicellular tissues involve tightly regulated and coordinated morphogenetic cell behaviours, such as shape changes, movement, and division, which are governed by subcellular machinery and involve coupling through short- and long-range signals. A key challenge in the fields of developmental biology, tissue engineering and regeneration is to understand how relationships between scales produce emergent tissue-scale behaviours. Recent advances in molecular biology, live-imaging and ex vivo techniques have revolutionised our ability to study these processes experimentally. To fully leverage these techniques and obtain a more comprehensive understanding of the causal relationships underlying tissue dynamics, computational modelling approaches are increasingly spanning multiple spatial and temporal scales, and are coupling cell shape, growth, mechanics and signalling. Yet such models remain technically challenging: modelling at each scale requires different areas of technical skills, while integration across scales necessitates the solution to novel mathematical and computational problems. This review aims to summarise recent progress in multiscale modelling of multicellular tissues and to highlight ongoing challenges associated with the construction, implementation, interrogation and validation of such models.
ARTICLE | doi:10.20944/preprints202106.0668.v1
Subject: Physical Sciences, Acoustics Keywords: Information dynamics; Multiscale analysis; Networks entropy; Network density matrix; Fungal networks
Online: 28 June 2021 (14:45:57 CEST)
Complex biological systems consist of large numbers of interconnected units, characterized by emergent properties such as collective computation. In spite of all the progress in the last decade, we still lack a deep understanding of how these properties arise from the coupling between the structure and dynamics. Here, we introduce the multiscale emergent functional state, which can be represented as a network where links encode the flow exchange between the nodes, calculated using diffusion processes on top of the network. We analyze the emergent functional state to study the distribution of the flow among components of 92 fungal networks, identifying their functional modules at different scales and, more importantly, demonstrating the importance of functional modules for information content of networks, quantified in terms of network spectral entropy. Our results suggest that the topological complexity of fungal networks guarantees the existence of functional modules at different scales keeping the information entropy, and functional diversity, high.
ARTICLE | doi:10.20944/preprints202001.0246.v1
Subject: Engineering, Civil Engineering Keywords: Cell Method (CM); Discrete Element Method (DEM); multiscale modeling; periodic composite continua
Online: 21 January 2020 (11:53:52 CET)
This paper addresses the study of the stress field in composites continua with the multiscale approach of the DECM (Discrete Element modeling with the Cell Method). The analysis focuses on composites consisting of a matrix with inclusions of various shapes, to investigate whether and how the shape of the inclusions changes the stress field. The purpose is to provide a numerical explanation for some of the main failure mechanisms of concrete, which is precisely a composite consisting of a cement-based matrix and aggregates of various shapes. Actually, while extensive experimental campaigns detailed the shape effect of concrete aggregates in the past, so far it has not been possible to model the stress field within the inclusions and on the interfaces accurately. The reason for this lies in the limits of the differential formulation, which is the basis of the most commonly used numerical methods. The Cell Method (CM), on the contrary, is an algebraic method that provides descriptions up to the micro-scale, independently of the presence of rheological discontinuities or concentrated sources. This makes the CM useful for describing the shape effect of the inclusions, on the micro-scale. When used together with a multiscale approach, it also models the macro-scale behavior of periodic composite continua, without losing accuracy on the micro-scale. The DECM uses discrete elements precisely to provide the CM with a multiscale approach.
ARTICLE | doi:10.20944/preprints202112.0266.v1
Subject: Materials Science, Nanotechnology Keywords: Density Functional Theory; Molecular Dynamics; Umbrella Sampling; Brownian Dynamics; Multiscale; Nanoparticle; Aggregation; Clustering
Online: 16 December 2021 (10:51:29 CET)
Titanium dioxide nanoparticles have risen concerns about their possible toxicity and the European Food Safety Authority recently banned the use of TiO2 nano-additive in food products. Following the intent of relating nanomaterials atomic structure with their toxicity without having to conduct large scale experiments on living organisms, we investigate the aggregation of titanium dioxide nanoparticles using a multi-scale technique: starting from ab initio Density Functional Theory to get an accurate determination of the energetics and electronic structure, we switch to classical Molecular Dynamics simulations to calculate the Potential of Mean Force for the connection of two identical nanoparticles in water; the fitting of the latter by a set of mathematical equations is the key for the upscale. Lastly, we perform Brownian Dynamics simulations where each nanoparticle is a spherical bead. This coarsening strategy allows studying the aggregation of a few thousand nanoparticles. Applying this novel procedure, we find three new molecular descriptors, namely, the aggregation free energy and two numerical parameters used to correct the observed deviation from the aggregation kinetic described by the Smoluchowski theory. Molecular descriptors can be fed into QSAR models to predict the toxicity of a material knowing its physicochemical properties, without having to conduct large scale experiments on living organisms.
ARTICLE | doi:10.20944/preprints201912.0014.v3
Subject: Engineering, Civil Engineering Keywords: Discrete Element Method (DEM); Cell Method (CM); multiscale modeling; periodic composite materials; nonlocality
Online: 10 February 2020 (10:09:46 CET)
This paper presents a new numerical method for multiscale modeling of composite materials. The new numerical model, called DECM, consists in a DEM (Discrete Element Method) approach of the Cell Method (CM) and combines the main features of both the DEM and the CM. In particular, it offers the same degree of detail as the CM, on the microscale, and manages the discrete elements individually such as the DEM—allowing finite displacements and rotations—on the macroscale. Moreover, the DECM is able to activate crack propagation until complete detachment and automatically recognizes new contacts. Unlike other DEM approaches for modeling failure mechanisms in continuous media, the DECM does not require prior knowledge of the failure position. Furthermore, the DECM solves the problems in the space domain directly. Therefore, it does not require any dynamic relaxation techniques to obtain the static solution. For the sake of example, the paper shows the results offered by the DECM for axial and shear loading of a composite two-dimensional domain with periodic round inclusions. The paper also offers some insights into how the inclusions modify the stress field in composite continua.
ARTICLE | doi:10.20944/preprints202106.0655.v1
Subject: Engineering, Automotive Engineering Keywords: Concrete; Mesoscale; Reduced order multiscale simulation; Microcracking; Micromechanics; Linear elastic fracture mechanics; Anisotropic damage
Online: 28 June 2021 (13:53:36 CEST)
Damage in concrete structures initiates as the growth of diffuse microcracks that is followed by damage localisation and eventually leads to structural failure. Weak changes such as diffuse microcracking processes are failure precursors. Identification and characterisation of these failure precursors at an early stage of concrete degradation and application of suitable precautionary measures will considerably reduce the costs of repair and maintenance. To this end, a reduced order multiscale model for simulating microcracking-induced damage in concrete at the mesoscale levelis proposed. The model simulates the propagation of microcracks in concrete using a two-scale computational methodology. First, a realistic concrete specimen that explicitly resolves the coarse aggregates in a mortar matrix was generated at the mesoscale. Microcrack growth in the mortar matrix is modelled using a synthesis of continuum micromechanics and fracture mechanics. Model order reduction of the two-scale model is achieved using clustering technique. Model predictions are calibrated and validated using uniaxial compression tests performed in the laboratory.
ARTICLE | doi:10.20944/preprints202101.0117.v1
Subject: Materials Science, Biomaterials Keywords: Thermal transport in nanocomposites; interfacial thermal conductance; graphene; borophene; multiscale modelling of thermal transport
Online: 6 January 2021 (13:26:46 CET)
Graphene and borophene are highly attractive two-dimensional materials with outstanding physical properties. In this study we employed a combined atomistic continuum multiscale modeling to explore the effective thermal conductivity of polymers nanocomposites made of PDMS polymer as the matrix and graphene and borophene as nanofillers. We first conduct classical molecular dynamics simulations to investigate the interfacial thermal conductance between graphene/PDMS and borophene/PDMS interfaces. Acquired results confirm that the interfacial thermal conductance between nanosheets and polymer increases from the single-layer to multilayered nanosheets and finally converges. The data provided by the atomistic simulations were then used in the finite element method simulations to evaluate the effective thermal conductivity of polymer nanocomposites at continuum level. We explore the effects of nanofillers type, their volume content, geometry aspect ratio and thickness on the nanocomposites effective thermal conductivity. As a very interesting finding, we show that borophene nanosheets, despite almost two orders of magnitude lower thermal conductivity than graphene, can yield very close enhancement in the effective thermal conductivity in comparison with graphene, particularly for low volume content and small aspect ratios and thicknesses. We conclude that for the polymer-based nanocomposites, significant improvement in the thermal conductivity can be reached by improving the bonding between the fillers and polymer or in another word enhancing the thermal conductance at the interface. By taking into account the high electrical conductivity of borophene, our results suggest borophene nanosheets as promising nanofillers to simultaneously enhance the polymers thermal and electrical conductivity.
ARTICLE | doi:10.20944/preprints201904.0322.v1
Subject: Engineering, Mechanical Engineering Keywords: aluminum profile surface defects; multiscale defect detection network; deep learning; average precision(AP); saliency maps
Online: 29 April 2019 (09:37:07 CEST)
Aluminum profile surface defects can greatly affect the performance, safety and reliability of products. Traditional human-based visual inspection is low accuracy and time consuming, and machine vision-based methods depend on hand-crafted features which need to be carefully designed and lack robustness. To recognize the multiple types of defects with various size on aluminum profiles, a multiscale defect detection network based on deep learning is proposed. Then, the network is trained and evaluated using aluminum profile surface defects images. Results show 84.6%, 48.5%, 96.9%, 97.9%, 96.9%, 42.5%, 47.2%, 100%, 100%, 43.3% average precision(AP) for the ten defect categories, respectively, with a mean AP of 75.8%, which illustrate the effectiveness of the network in aluminum profile surface defects detection. In addition, saliency maps also show the feasibility of the proposed network.
ARTICLE | doi:10.20944/preprints202206.0312.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: refined multiscale entropy; sample entropy; bubble entropy; adaptive complex system; pressure ulcer; machine learning; body temperature
Online: 22 June 2022 (09:52:15 CEST)
This study examined the association between pressure injuries and complexity of abdominal temperature measured in residents of a nursing facility. The temperature served as a proxy measure for skin thermoregulation. Refined multiscale sample entropy and bubble entropy were used to measure the complexity of the temperature time series measured over two days at 1-minute intervals. Robust summary measures were derived for the multiscale entropies and used in predictive models for pressure injuries that were built with adaptive lasso regression and neural networks. Both types of entropies were lower in the group of participants with pressure injuries (n=11) relative to the group of non-injured participants (n=15). This was generally true at the longer temporal scales, with the effect peaking at scale τ=23 minutes. Predictive models for pressure injury on the basis of refined multiscale sample entropy and bubble entropy yielded 92% accuracy, outperforming predictions based on any single measure of entropy. Combining entropy measures with a widely used risk assessment score led to the best prediction accuracy. Complexity of abdominal temperature series could therefore serve as an indicator of risk of pressure injury.
Subject: Medicine & Pharmacology, Other Keywords: Reproducibility, Mathematical Modeling, Multiscale Modeling, Translational Research, Biomedical Research, Experimental Biology, Clinical Research Article Type: Essay
Online: 23 May 2018 (16:18:52 CEST)
The “Crisis of Reproducibility” has received considerable attention both within the scientific community and without. While factors associated with scientific culture and practical practice are most often invoked, I propose that the Crisis of Reproducibility is ultimately a failure of generalization with a fundamental scientific basis in the methods used for biomedical research. The Denominator Problem describes how limitations intrinsic to the two primary approaches of biomedical research, clinical studies and pre-clinical experimental biology, lead to an inability to effectively characterize the full extent of biological heterogeneity, which compromises the task of generalizing acquired knowledge. Drawing on the example of the unifying role of theory in the physical sciences, I propose that multi-scale mathematical and dynamic computational models, when mapped to the modular structure of biological systems, can serve a unifying role as formal representations of what is conserved and similar from one biological context to another. This ability to explicitly describe the generation of heterogeneity from similarity addresses the Denominator Problem and provides a scientific response to the Crisis of Reproducibility.
ARTICLE | doi:10.20944/preprints202104.0475.v1
Subject: Medicine & Pharmacology, Allergology Keywords: drug repurposing; virtual screening; multiscale; multitargeting; polypharmacology; computational biology; drug repositioning; structural bioinformatics; molecular docking; proteomic signature
Online: 19 April 2021 (12:22:05 CEST)
Drug repurposing, the practice of utilizing existing drugs for novel clinical indications, has tremendous potential for improving human health outcomes and increasing therapeutic development efficiency. The goal of multidisease multitarget drug repurposing, also known as shotgun drug repurposing, is to develop platforms that assess the therapeutic potential of each existing drug for every clinical indication. Our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget repurposing implements several pipelines via large scale modelling and simulation of interactions between comprehensive libraries of drugs/compounds and protein structures. In these pipelines, each drug is described by an interaction signature that is then compared to all other signatures that are then sorted and ranked based on similarity. Pipelines within the platform are benchmarked based on their ability to recover known drugs for all indications in our library, and predictions are generated based on the hypothesis that (novel) drugs with similar signatures may be repurposed for the same indication(s). The drug-protein interactions in the platform used to create the drug-proteome signatures may be determined by any screening or docking method but the primary approach used thus far has been an in house similarity docking protocol. In this study, we calculated drug-proteome interaction signatures using the publicly available molecular docking method Autodock Vina and created hybrid decision tree pipelines that combined our original bio- and cheminformatic approach with the goal of assessing and benchmarking their drug repurposing capabilities and performance. The hybrid decision tree pipeline outperformed the corresponding two docking-based pipelines it was synthesized from, yielding an average indication accuracy of 13.3% at the top10 cutoff (the most stringent), relative to 10.9% and 7.1% for its constituent pipelines, and a random control accuracy of 2.2%. We demonstrate that docking based virtual screening pipelines have unique performance characteristics and that the CANDO shotgun repurposing paradigm is not dependent on a specific docking method. Our results also provide further evidence that multiple CANDO pipelines can be synthesized to enhance drug repurposing predictive capability relative to their constituent pipelines. Overall, this study indicates that pipelines consisting of varied docking based signature generation methods can capture unique and useful signal for accurate comparison of drug-proteome interaction signatures, leading to improvements in the benchmarking and predictive performance of the CANDO shotgun drug repurposing platform.
ARTICLE | doi:10.20944/preprints201612.0115.v1
Subject: Materials Science, General Materials Science Keywords: discrete element method; hypervelocity impact; debris cloud; fragmentation; space debris; multiscale modeling; computer simulation; high performance computing
Online: 23 December 2016 (10:21:21 CET)
In this paper we introduce a computational model for the simulation of hypervelocity impact (HVI) phenomena which is based on the Discrete Element Method (DEM). Our paper constitutes the first application of DEM to the modeling and simulating of impact events for velocities beyond 5 kms−1. We present here the results of a systematic numerical study on HVI of solids. For modeling the solids, we use discrete spherical particles that interact with each other via potentials. In our numerical investigations we are particularly interested in the dynamics of material fragmentation upon impact. We model a typical HVI experiment configuration where a sphere strikes a thin plate and investigate the properties of the resulting debris cloud. We provide a quantitative computational analysis of the resulting debris cloud caused by impact and a comprehensive parameter study by varying key parameters of our model. We compare our findings from the simulations with recent HVI experiments performed at our institute. Our findings are that the DEM method leads to very stable, energy–conserving simulations of HVI scenarios that map the experimental setup where a sphere strikes a thin plate at hypervelocity speed. Our chosen interaction model works particularly well in the velocity range where the local stresses caused by impact shock waves markedly exceed the ultimate material strength.
Subject: Life Sciences, Biochemistry Keywords: CA3-CA1 synapses; NMDA; AMPA; systems biology; multiscale modeling; synaptic plasticity; long term potentiation; long term depression; hippocampus
Online: 8 January 2021 (13:17:31 CET)
Inside hippocampal circuits, neuroplasticity events that individual cells may undergo during synaptic transmissions occur in the form of Long Term Potentiation (LTP) and Long Term Depression (LTD). The high density of NMDA receptors expressed on the surface of the dendritic CA1 spines confers to hippocampal CA3-CA1 synapses, the ability to easily undergo NMDA-mediated LTP and LTD, that is essential for some forms of explicit learning in mammals. Providing a comprehensive kinetic model that can be used for running computer simulations of the synaptic transmission process is currently a major challenge. Here, we propose a compartmentalized kinetic model for CA3-CA1 synaptic transmission. Our major goal was to tune our model in order to predict the functional impact caused by disease associated variants of NMDA receptors related to severe cognitive impairment. Indeed, for variants Glu413Gly and Cys461Phe, our model predicts negative shifts in the glutamate affinity and changes in the kinetic behavior, consistent with experimental data. These results pinpoint to the predictive power of this multiscale viewpoint, which aims to integrate the quantitative kinetic description of large interaction networks typical of system biology approaches with a focus on the quality of few, key, molecular interactions typical of structural biology ones.
ARTICLE | doi:10.20944/preprints201612.0054.v1
Subject: Mathematics & Computer Science, Applied Mathematics Keywords: computational model; lymph node; multiscale structure; vascular network; fibroblastic reticular cells; conduit network; lymph flow; destruction of conduits
Online: 9 December 2016 (10:19:20 CET)
In this study we discuss critical issues in modelling the structure and function of lymph nodes (LNs), with emphasis on how LN physiology is related to its multi-scale structural organization. In addition to macroscopic domains such as B-cell follicles and the T cell zone, there are vascular networks which play a key role in the delivery of information to the inner parts of the LN, i.e., the conduit and blood microvascular networks. We propose object-oriented computational algorithms to model the 3D geometry of the fibroblastic reticular cell (FRC) network and the microvasculature. Assuming that a conduit cylinder is densely packed with collagen fibers, the computational flow study predicted that the diffusion should be a dominating process in mass transport than convective flow. The geometry models are used to analyze the lymph flow properties through the conduit network in unperturbed- and damaged states of the LN. The analysis predicts that elimination of up to 60–90 % of edges is required to stop the lymph flux. This result suggests a high degree of functional robustness of the network.
ARTICLE | doi:10.20944/preprints201910.0326.v1
Subject: Biology, Physiology Keywords: center of pressure (cop); average entropy (ae); entropy of entropy (eoe); multiscale entropy (mse), inverted u curve; biological disorder; biological complexity
Online: 29 October 2019 (10:01:12 CET)
Static standing postural stability has been measured by multiscale entropy (MSE), which is used to measure complexity. In this study, we used the average entropy (AE) to measure the static standing postural stability, as AE is a good measure of disorder. The center of pressure (COP) trajectories were collected from 11 subjects under four kinds of balance situation, from stable to unstable: bipedal with open eyes, bipedal with closed eyes, unipedal with open eyes, and unipedal with closed eyes. The AE, entropy of entropy (EoE), and MSE methods were used to analyze these COP data, and EoE was found to be a good measure of complexity. The AE of the 11 subjects sequentially increased by 100%as the balance situations progressed from stable to unstable, but the results of EoE and MSE did not follow this trend. Therefore, AE, rather than EoE or MSE, is a good measure of static standing postural stability. Furthermore, the comparison of EoE and AE plots exhibited an inverted U curve, which is another example of a complexity versus disorder inverted U curve.
REVIEW | doi:10.20944/preprints202101.0388.v1
Subject: Life Sciences, Biochemistry Keywords: Thymic selection; T-cell development; T-cell receptor (TCR); mathematical modelling; multiscale models; complex systems; ordinary differential equations (ODE); agent-based models.
Online: 19 January 2021 (16:39:50 CET)
The thymus hosts the development of a specific type of adaptive immune cells called T cells. T cells orchestrate the adaptive immune response through recognition of antigen by the highly variable T-cell receptor (TCR). T-cell development is a tightly coordinated process comprising lineage commitment, somatic recombination of Tcr gene loci and selection for functional, but non-self-reactive TCRs, all interspersed with massive proliferation and cell death. Thus, the thymus produces a pool of T cells throughout life capable of responding to virtually any exogenous attack while preserving the body through self-tolerance. The thymus has been of considerable interest to both immunologists and theoretical biologists due to its multiscale quantitative properties, bridging molecular binding, population dynamics and polyclonal repertoire specificity. Here, we review mathematical modelling strategies that were reported to help understand the flexible dynamics of the highly dividing and dying thymic cell populations. Furthermore, we summarize the current challenges to estimating in vivo cellular dynamics and to reaching a next-generation multiscale picture of T-cell development.
ARTICLE | doi:10.20944/preprints202103.0581.v1
Subject: Biology, Anatomy & Morphology Keywords: Alpine ecology; Arabis alpina; Digital Elevation Models (DEMs); Light Detection and Ranging (LiDAR); Multiscale; Photogrammetry; Spatial scale; Species distribution models (SDM); Terrain attributes; Very-high resolution
Online: 24 March 2021 (12:30:37 CET)
The vulnerability of alpine environments to climate change presses an urgent need to accurately model and understand these ecosystems. Popularity in use of digital elevation models (DEMs) to derive proxy environmental variables has increased over the past decade, particularly as DEMs are relatively cheaply acquired at very high resolutions (VHR; <1m spatial resolution). Here, we implement a multiscale framework and compare DEM-derived variables produced by Light Detection and Ranging (LiDAR) and stereo-photogrammetry (PHOTO) methods, with the aims of assessing their relevance and utility in species distribution modelling (SDM). Using a case study on the arctic-alpine plant Arabis alpina in two valleys in the western Swiss Alps, we show that both LiDAR and PHOTO technologies can be relevant for producing DEM-derived variables for use in SDMs. We demonstrate that PHOTO DEMs rivalled the accuracy of LiDAR, putting the current paradigm of LiDAR being the more accurate of the two methods into question. We obtained DEMs at spatial resolutions of 6.25cm-8m for PHOTO and 50cm-32m for LiDAR, where we determined that the optimal spatial resolutions of DEM-derived variables in SDM were between 1 and 32m, depending on the variable and site characteristics. We found that the reduced extent of PHOTO DEMs altered the calculations of all derived variables, which had particular consequences on their relevance at the site with heterogenous terrain. However, for the homogenous site, we found that SDMs based on PHOTO-derived variables generally had higher predictive powers than those derived from LiDAR at matching resolutions. From our results, we recommend carefully considering the required DEM extent to produce relevant derived variables. We also advocate implementing a multiscale framework to appropriately assess the ecological relevance of derived variables, where we caution against the use of VHR-DEMs finer than 50cm in such studies.