相关论文: Medium effects on the selection of sequences foldi…
The overall structure of the transition state and intermediate ensembles experimentally observed for Dihydrofolate Reductase and Interleukin-1beta can be obtained utilizing simplified models which have almost no energetic frustration. The…
The effect of a "pore-size" length-scale parameter l on compaction of grounds with fluid inclusions is studied. They are modelled as continua endowed with micro-structure by means of the macro-modelling procedure proposed in [2]. We show…
This article delves into the micro-macro modeling of polymeric fluids, considering various microscopic potential energies, including the classical Hookean potential, as well as newly proposed modified Morse and Elastic-plastic potentials.…
This research paper comprehensively explores the effects of molecular weight and chain architecture on the interfacial and thermodynamic properties of cyclic and linear polymer blends. Utilizing the Kremer-Grest bead-spring model, the study…
Homologous proteins have similar three-dimensional structures and biological functions that shape their sequences. The resulting coevolution-driven correlations underlie methods from Potts models to AlphaFold, which infer protein structure…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
The surface a thin-film is attached to and the surrounding monolayer causes geometrical confinement of a interrogated molecule; we look at the base case of a SC$_{18}H_{37}$ in a SC$_{18}H_{37}$ monolayer on Au[111]. Normal mode analysis…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
Instead of conformation states of single residues, refined conformation states of quintuplets are proposed to reflect conformation correlation. Simple hidden Markov models combining with sliding window scores are used for predicting…
The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging…
In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…
Experiments on supported lipid bilayers featuring liquid ordered/disordered domains have shown that the spatial arrangement of the lipid domains and their chemical composition are strongly affected by the curvature of the substrate.…
We investigate the property of the high-density nuclear matter probed by the nucleus-nucleus elastic scattering in the framework of the double-folding (DF) model with the complex $G$-matrix interaction. The medium effect including…
We study the porous medium equation (PME) in one space dimension in presence of additive non-conservative white noise, and interpreted as a stochastic growth equation for the height field of an interface. We predict the values of the two…
How the geometry of nano-sized confinement affects dynamics of biomaterials is interesting yet poorly understood. An elucidation of structural details upon nano-sized confinement may benefit manufacturing pharmaceuticals in biomaterial…