Evaporation studies of water using classical molecular dynamics simulations are largely limited due to its high computational expense. We aim at addressing the computational issues by developing a coarse grain model for evaporation of water on solid surfaces by combining four water molecules into a single bead. Most commonly used mono atomic pair potentials like Lennard Jones, Morse, Mie and three body potential like Stillinger-Weber are optimized using a combination of Genetic algorithm and Nelder-Mead algorithm. Among them, Stillinger-Weber based model shows excellent agreement of density and Enthalpy of vaporization with experimental results for a wide range of temperatures. Further, the new water model is used to simulate contact angle of water and thin film evaporation from surfaces with different wettabilities.

A class $\mathfrak{M}$ $$ of coarse spaces is called a variety if $\mathfrak{M}$ $$ is closed under formation of subspaces, coarse images and products. We classify the varieties of coarse spaces and, in particular, show that if a variety $\mathfrak{M}$ $$ contains an unbounded metric space then $\mathfrak{M}$ is the variety of all coarse spaces.

A class $\mathfrak{M}$ $$ of coarse spaces is called a variety if $\mathfrak{M}$ $$ is closed under formation of subspaces, coarse images and products. We classify the varieties of coarse spaces and, in particular, show that if a variety $\mathfrak{M}$ $$ contains an unbounded metric space then $\mathfrak{M}$ is the variety of all coarse spaces.

Molecular modeling is widely utilized in subjects including but not limited to physics, chemistry, biology, materials science and engineering. Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, Most of important methodological advancements in more than half century of molecule modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science based on force fields parameterization by coarse graining, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes "dividing and conquering" and/or "caching" in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but no transferability is available. Deep learning has been utilized to realize more efficient and accurate ways of "dividing and conquering" and "caching" along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science and a third class of algorithm that facilitates molecular modeling through partially transferable in resolution "caching" of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for "dividing and conquering" and "caching" in complex molecular systems.

Borneol and menthol were two terpenes wildly used as penetrate enhancer in transdermal drug delivery. To explore their penetration enhancement effect towards hydrophilic drug, 5-FU was selected as model drug. A method combined vitro permeation studies and coarse grain molecular dynamics was used to investigate their penetration enhancement effect towards 5-FU. As a result, although both borneol and menthol showed a penetration enhancement effect towards 5-FU, they differed a lot in the penetration enhancement mechanism, which was also thought to account for their different penetration enhancement effect. As for menthol, SC bilayer disrupting effect seemed to be its main mechanism. While for borneol, its mechanism seemed to be more complicated. Except for disrupting the SC bilayer, it could also increase the permeation of 5-FU by enhancing the diffusion rate of 5-FU or inducing the formation of transient pore. All of this enable us a molecular understanding of borneol and menthol’s penetration enhancement effect towards hydrophilic drug, which might provide some guidance in the latter research and application.

Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this mini-review, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions and, on other hand, highly simplified structure-based Elastic Network Models of protein flexibility. In contrast to classical Molecular Dynamics the modeling strategies discussed here allow quite accurate modeling of much larger systems and longer time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.

The addition of active seed for increasing the precipitation rate leads to the formation of fine Al(OH)3 particles that complicates separation of solid from the mother liquor. In this study, the enhanced precipitation of coarse Al(OH)3 from sodium aluminate solution using active agglomerated seed was investigated. Aluminum salt (Al2(SO4)3) were used for active agglomerated seed precipitation at the initial of the process. About 50% of precipitation rate was obtained when these agglomerates were used as a seed in the amount of 20 g L–1 at 25 °C within 10 h. The agglomerated active seed and precipitate samples were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM) and Fourier-transform infrared spectroscopy (FTIR). SEM images showed that agglomerates consist of flake-like particles that can be stick together by bayerite (β-Al(OH)3) acting as a binder. The precipitation temperature above 35 °C and the high concentration of free alkali (αk > 3) lead to the agglomerates refinement that can be associated with the bayerite dissolution.

In this paper, feasibility of the initial alignment of the gyro-free inertial navigation system (GF-INS) is investigated. Initial roll and initial pitch are obtained as the conventional INS since centripetal acceleration is very small. Relation between initial heading and accelerometers’ outputs of the gyro-free inertial measurement unit (GF-IMU) is derived. It is determined from the relation whether initial heading can be obtained in 15 GF-IMUs which have been presented in research literatures. The relationship between the accelerometer errors of GF-IMU and the initial heading error is derived. When gyros are additionally attached in one axis or two axes of the body frame, it is investigated that initial heading can be obtained. The initial heading error is also calculated from the accelerometer errors and the gyroscope errors. The results show that the initial heading from only accelerometer outputs of the GF-IMU cannot be used in the GF-INS since the error is too large. It can also be seen from the results that the initial heading can be used in the GF-INS if two gyroscopes are additionally attached to the roll and pitch axes of the body frame.

This paper mainly explores the feasibility of using desert sand (DS) and recycled aggregate in cement stabilized base. Recycled coarse aggregate (RCA) and DS serve as the substitutes of natural coarse and fine aggregates, respectively, in cement stabilized base. A four-factor and four-level orthogonal test is designed to analyze the unconfined compressive strength, splitting tensile strength, and compressive resilient modulus. Furthermore, this paper investigates the effects of cement content, fly ash (FA) replacement rate, RCA replacement rate, and DS replacement rate on the road performance of cement stabilized base composing of RCA and DS. The test results reveal that the performance of cement stabilized base with partial RCA instead of natural coarse aggregate (NCA) and partial DS instead of natural fine aggregate satisfy the road use. Meanwhile, DS is beneficial to improve the strength of cement stabilized base. The correlation and microscopic analyses of the test results imply the feasibility of applying DS and recycled aggregate to cement stabilized base. It is hoped that this paper can offer a solid theoretical foundation for promoting the application of DS and recycled aggregate in road engineering.

The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling disordered protein interactions and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein-peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein-peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution and studies of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution.

In precision grinding of hard and brittle materials, coarse-grained diamond grinding wheels are increasingly favored for their efficiency and contour accuracy. However, challenges in dressing these grinding wheels have hindered their widespread adoption. In this paper, the effects of dressing parameters on the surface profile and morphological characteristics of electroplated coarse-grained diamond were studied, thereby optimizing the dressing accuracy and dressing efficiency of the coarse-grained diamond grinding wheel. Models for the surface morphology of the large-grained diamond grinding wheel and its grinding surface were established. With a focus on optimizing dressing accuracy, we explored how the grain’s protruding height post-dressing affects the surface morphology of both the diamond grinding wheel and the grinding surface. The model’s accuracy was verified by electroplated coarse-grained diamond grinding wheel grinding experiments with different grain protrusion heights, and the causes of surface morphology formation were analyzed based on morphological characteristic parameters such as surface roughness and surface height difference. The results showed that compared with the undressed grinding wheel, the surface roughness Sa and Sq of the workpiece by the dressing wheel are reduced by 97.75%−99.77% and 97.57%−99.73%, respectively. Precision dressing enables the surface roughness of the electroplated coarse-grained diamond grinding wheel to reach nanometer levels, enhancing its feasibility and application potential.

Image segmentation is a new challenge prob- lem in medical application. The use of medical imaging has become an integral part of research, as it allows us to see inside the human body without surgical intervention. Many researcher have studied brain segmentation. One stage method is used to segment the brain tissues. In this paper, we proposed the multi-stage generative ad- versarial network to solve the problem of information loss in the one-stage. We utilize the coarse-to-fine to improve brain segmentation using multi-stage generative adversar- ial networks (GAN). In the first stage, our model generated a coarse outline for (i) background and (ii) brain tissues. Then, in the second stage, the model generated outline for (i) white matter (WM), (ii) gray matter (GM) and (iii) cerebrospinal fluid (CSF). A good result can be achieved by fusing the coarse outline and refine outline. We conclude that our model is more efficient and accu- rate in practice for both infant and adult brain segmenta- tion. Moreover, we observe that multi-stage model is faster than prior models. To be more specific, the main goal of multi-stage model is to see the performance of the model in a few shot learning case where a few labeled data are available. For medical image, this proposed model can work in a wide range of image segmentation where the convolution neural networks and one-stage methods have failed.

Mapping vegetation species is critical to facilitate related quantitative assessment, and for invasive plants mapping their distribution is important to enhance monitoring and controlling activities. Integrating high resolution multispectral remote sensing (RS) image and lidar (light detection and ranging) point clouds can provide robust features for vegetation mapping. However, using multiple source of high-resolution RS data for vegetation mapping at large spatial scale can be both computationally and sampling intensive. Here we designed a two-step classification workflow to decrease computational cost and sampling effort, and to increase classification accuracy by integrating multispectral and lidar data to derive spectral, textural, and structural features for mapping target vegetation species. We used this workflow to classify kudzu, an aggressive invasive vine, in the entire Knox County (1,362 km2) of Tennessee, the United States. Object-based image analysis was conducted in the workflow. The first-step classification used 320 kudzu samples and extensive coarsely labeled samples (based on national land cover) to generate an overprediction map of kudzu using random forest (RF). For the second step, 350 samples were randomly extracted from the overpredicted kudzu and labeled manually for the final prediction using RF and support vector machine (SVM). Computationally intensive features were only used for the second-step classification. SVM had constantly better accuracy than RF, and the Producer’s Accuracy, User’s Accuracy, and Kappa for the SVM model on kudzu was 0.94, 0.96, and 0.90, respectively. SVM predicted 1010 kudzu patches covering 1.29 km2 in Knox County. We found the sample size of kudzu used for algorithm training impacted the accuracy and number of kudzu predicted. The proposed workflow could also improve sampling efficiency and specificity. Our workflow had much higher accuracy than the traditional method conducted in this research, and could be easily implemented to map kudzu in other regions or other vegetation species.

Object-level Simultaneous Localization and Mapping (SLAM) has gained popularity in recent years since it can provide a means for intelligent robot-to-environment interactions. However, most of these methods assume that the distribution of the errors is gaussian. This assumption is not valid under many circumstances. Further, these methods use a delayed initialization of the objects in the map. During this delayed period, the solution relies on the motion model provided by an Inertial Measurement Unit (IMU). Unfortunately, the errors tend to accumulate quickly due to the dead-reckoning nature of these motion models. Finally, the current solutions depend on a set of salient features on the object’s surface and not the object’s shape. This research proposes an accurate object-level solution to the SLAM problem with a 4.1 to 13.1 cm error in the position (0.005 to 0.021 of the total path). The developed solution is based on Rao-blackwellized Particle Filtering (RBPF) that does not assume any predefined error distribution for the parameters. Further, the solution relies on the shape and thus can be used for objects that lack texture on their surface. Finally, the developed tightly coupled IMU/camera solution is based on an undelayed initialization of the objects in the map.