相关论文: Influence of pH and sequence in peptide aggregatio…
Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to…
A hybrid model of molecular dynamics and continuum mechanics is introduced to study a system of vertically shaken granular layers. Despite the simplicity the model shows pattern formation in the granular layers due to the formation of…
Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative…
In this work, the effects of finite size on the determination of the three-phase coexistence temperature ($T_3$) of carbon dioxide (CO$_2$) hydrate have been studied by molecular dynamic simulations and using the direct coexistence…
Many cellular organelles are membrane-bound structures with complex membrane composition and shape. Their shapes have been observed to depend on the metabolic state of the organelle, and the mechanisms that couple biochemical pathways and…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
We perform a two-dimensional molecular-dynamics study of a model for sheared bidisperse granular systems under conditions of simple shear and Poiseuille flow. We propose a mechanism for particle-size segregation based on the observation…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
We study the medium effects on the selection of sequences in protein folding by taking account of the surface potential in HP-model. Our analysis on the proportion of H and P monomers in the sequences gives a direct interpretation that the…
Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…
In this work, we study whether enforcing strict compositional structure in sequence embeddings yields meaningful geometric organization when applied to protein-protein interaction networks. Using Event2Vec, an additive sequence embedding…
Understanding interactions between microparticles and lipid membranes is of increasing importance, especially for unraveling the influence of microplastics on our health and environment. Here, we study how a short-ranged adhesive force…
The structure and mechanical properties of a simple two-dimensional model of a cohesive powder are investigated by molecular dynamics simulations. Micromechanical ingredients involve elasticity, friction, a short range attraction and,…
Cells contain multiple condensates which spontaneously form due to the heterotypic interactions between their components. Although the proteins and disordered region sequences that are responsible for condensate formation have been…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…
We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of…
We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during…
Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…