Related papers: Characterization of Protein Folding by Dominant Re…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
The relevance of various residue positions for the stability and the folding characteristics of the prion protein are investigated by using molecular dynamics simulations of models exploiting the topology of the native state. Highly…
A protein is a linear chain containing a set of amino acids, which folds on itself to create a specific native structure, also called the minimum energy conformation. It is the native structure that determines the functionality of each…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
The Bin Packing Problem (BPP) has attracted enthusiastic research interest recently, owing to widespread applications in logistics and warehousing environments. It is truly essential to optimize the bin packing to enable more objects to be…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Reaction-diffusion (RD) systems provide fundamental models for understanding self-organized spatiotemporal patterns across natural and engineered settings, yet reliable parameter estimation remains challenging, particularly when…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Backdoor attacks, which maliciously control a well-trained model's outputs of the instances with specific triggers, are recently shown to be serious threats to the safety of reusing deep neural networks (DNNs). In this work, we propose an…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
Learning domain adaptive policies that can generalize to unseen transition dynamics, remains a fundamental challenge in learning-based control. Substantial progress has been made through domain representation learning to capture…
We demonstrate that when two colliding nuclei approach each other, their quantum vibrations are damped near the touching point. We show that this damping is responsible for the fusion hindrance phenomena measured in the deep sub-barrier…
Computational prediction of enzymatic reactions represents a crucial challenge in sustainable chemical synthesis across various scientific domains, ranging from drug discovery to materials science and green chemistry. These syntheses rely…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
Identifying T-cell receptors (TCRs) that interact with antigenic peptides provides the technical basis for developing vaccines and immunotherapies. The emergent deep learning methods excel at learning antigen binding patterns from known…
Boron phosphide (BP) is a (super)hard semiconductor constituted of light elements, which is promising for high demand applications at extreme conditions. The behavior of BP at high temperatures and pressures is of special interest but is…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…