相关论文: Transfer matrix solution of the Wako-Sait\^o-Mu\~n…
A simple statistical mechanical model proposed by Wako and Sait$\hat{\rm o}$ has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Mu$\tilde{\rm n}$oz and Eaton and has…
A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
The weighted ensemble (WE) simulation strategy provides unbiased sampling of non-equilibrium processes, such as molecular folding or binding, but the extraction of rate constants relies on characterizing steady state behavior.…
Variable charge models (e.g., EEM, QEq, ES+) in reactive molecular dynamics simulations often inherently impose a global charge transfer between atoms (approximating each system as ideal metal). Consequently, most surface processes (e.g.,…
We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…
A simple statistical mechanical approach for studying multilayer adsorption of interacting polyatomic adsorbates (k-mers) has been presented. The new theoretical framework has been developed on a generalization in the spirit of the…
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically…
The modified static exchange model (MSEM) recently introduced by Ray [1] to study two-atomic collision processes at low and cold-energies, is used for detailed analysis of the long-range effects due to induced dipole-dipole van der Waals…
The Hatsugai-Kohmoto interaction model has gained a lot of attention in recent years, due to the fact it is exactly solvable in momentum space in any dimension while capturing some key features of the Mott phase. Here a one-dimensional…
We apply the Wako-Saito-Munoz-Eaton model to the study of Myotrophin, a small ankyrin repeat protein, whose folding equilibrium and kinetics have been recently characterized experimentally. The model, which is a native-centric with binary…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
The Standard Model of electroweak interactions is shown to include a gauge theory for the observed scalar and pseudoscalar mesons. This is done by exploiting the consequences of embedding the SU(2)left X U(1) group into the chiral group of…
Simulating long-range interactions remains a significant challenge for molecular machine learning potentials due to the need to accurately capture interactions over large spatial regions. In this work, we introduce FieldMACE, an extension…
An ab-initio analysis based on coupled mode theory (CMT) is applied to describe the interaction dynamics of high dielectric resonators (DRs) with its containing aqueous solution. We prove that the coupling mechanism is reciprocal. Such…
We consider diffusion of particles on a lattice in the so-called dynamical mean-field regime (memory effects are neglected). Interactions are local, that is, only among particles at the same lattice site. It is shown that a statistical…
We show that spectral fluctuation of interaction matrices of yeast a core protein interaction network and a metabolic network follows the description of the Gaussian orthogonal ensemble (GOE) of random matrix theory (RMT). Furthermore, we…
We present a simple yet generic model for the behavior of a system of many surface-attached flexible polymers with rigid side chains. Beyond its potential application in describing the dynamics of the extracellular matrix of mammalian…
Realistic physical systems are characterised by emergent interactions across multiple length and time scales, posing a significant challenge for predictive machine learning (ML) models. Most scientific ML models focus on a narrow range of…
A recent simplified transfer matrix solution of the two-dimensional Ising model on a square lattice with periodic boundary conditions is generalized to periodic-antiperiodic, antiperiodic-periodic and antiperiodic-antiperiodic boundary…