Related papers: Impulse-Response Approach to Elastobaric Model for…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
In extending the conventional dynamic models, we consider a simple model to account for the environment fluctuations of particle atoms in a protein system and derive the elastic incoherent structure factor (EISF) and the incoherent…
The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where…
Protein dynamics play a crucial role in protein biological functions and properties, and their traditional study typically relies on time-consuming molecular dynamics (MD) simulations conducted in silico. Recent advances in generative…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…
We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM…
Soft biological tissues often have complex mechanical properties due to variation in structural components. In this paper, we develop a novel UNet-based neural network model for inversion in elasticity (El-UNet) to infer the spatial…
We consider a coarse-grained polymer model in order to investigate the origin of a recently discovered negative energy-related contribution to the elastic modulus $G(T)$ of rubber-like gels. From this model, we are able to compute an exact…
Current state-of-the-art generative models map noise to data distributions by matching flows or scores. A key limitation of these models is their inability to readily integrate available partial observations and additional priors. In…
We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three…
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the…
The diffraction slope parameter is investigated for elastic proton-proton and proton-antiproton scattering based on the all available experimental data at low momentum transfer values. Energy dependence of the elastic diffraction slopes is…
We calculate differential cross sections for proton-nucleus elastic scattering by using a Glauber theory in the optical limit approximation and nucleon distributions that can be obtained in the framework of macroscopic nuclear models in a…
Elastic scattering data for $^{141}$Pr($\alpha$,$\alpha$)$^{141}$Pr have been analyzed to derive a new energy-dependent local potential for the $^{141}$Pr-$\alpha$ system. This potential is used successfully to predict the cross section of…
We probe, using a model system, elastic and kinetic energies for sheared granular materials. For large enough $P/E_y$ (pressure/Young's modulus) and $P/\rho v^2$ ($P/$kinetic energy density) elastic dominates kinetic energy, and energy…
Elastic models of the glass transition relate the relaxation dynamics and the elastic properties of structural glasses. They are based on the assumption that the relaxation dynamics occurs through activated events in the energy landscape…
The ratio of elastic to total proton cross sections is related to the darkness of the spatial profile of inelastic interactions by a single parameter in the framework of a simple analytical model. Their critical values at LHC energies are…