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Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
Considering high-temperature heating, the equations of transient heat conduction model require an adaptation, i.e. the dependence of thermophysical parameters of the model on the temperature is to be identified for each specific material to…
We develop an approach to liquid thermodynamics based on collective modes. We perform extensive molecular dynamics simulations of noble, molecular and metallic liquids and provide the direct evidence that liquid energy and specific heat are…
We explore how the thermodynamic properties and dynamics of a self-interstitial prismatic dislocation loop are affected by microscopic-scale variations in its geometric configuration, an aspect that rarely received attention in literature.…
The 1mm roundworm C. elegans is a model organism used in many sub-areas of biology to investigate different types of biological processes. In order to complement the n-vivo analysis with computer-based investigations, several methods have…
The interplay of slow dynamics and thermodynamic features of dense liquids is studied by examinining how the glass transition changes depending on the presence or absence of Lennard-Jones-like attractions. Quite different thermodynamic…
We derive a class of thermodynamically consistent variants of Maxwell/Oldroyd-B type models for viscoelastic fluids. In particular, we study the models that allow one to consider temperature dependent material coefficients. This naturally…
Thermal preferences vary from person to person and may change over time. The main objective of this paper is to sequentially pose intelligent queries to occupants in order to optimally learn the indoor air temperature values which maximize…
My analysis uses methods developed for data mining microarray experiments, adapted for ageing research. Methods bridge knowledge of statistical mechanics with data mining methods developed in statistical mathematics. Analyses can reveal how…
Understanding physical rules underlying collective motions requires perturbation of controllable parameters in self-propelled particles. However, controlling parameters in animals is generally not easy, which makes collective behaviours of…
In the past years, a remarkable mapping has been found between the dynamics of a population of M individuals undergoing random mutations and selection, and that of a single system in contact with a thermal bath with temperature 1/M. This…
Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…
We study the dissipative thermodynamics of vortex lines in layered superconductors within a simple string model in the dilute limit of negligible vortex interactions and compute the specific heat $C_v$ in presence of arbitrary dissipation.…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
The dynamics of complex systems generally include high-dimensional, non-stationary and non-linear behavior, all of which pose fundamental challenges to quantitative understanding. To address these difficulties we detail a new approach based…
We experimentally studied the locomotion of the nematode C. elegans in both fluidic and granular media. In this fluid dynamics video, we show the motility gaits of the nematode in these two environments. The motility of the nematode C.…
Recent advances in physics-augmented neural networks have enabled thermodynamically consistent data-driven constitutive modeling of complex inelastic materials. Most existing approaches, however, implicitly adopt a specific thermodynamic…
We establish three partial differential equation models describing the thermodynamics of the fluid, by combining the energetic variational approach, appropriate constitutive relations, and classical thermodynamics laws. What is more, by…