相关论文: Detection of residual native state entropy changes…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of…
In two dimensional magnets, the interplay of thermal fluctuations and spin anisotropy control the existence of long-range magnetic order. In the van der Waals antiferromagnets FePX$_3$, orbital degeneracy in the $t2g$ levels of the…
We investigate the structural and magnetic phase transitions in EuTi1-xNbxO3 with synchrotron powder X-ray diffraction (XRD), resonant ultrasound spectroscopy (RUS), and magnetization measurements. Upon Nb-doping, the Pm-3m to I4/mcm…
We propose the entropy of random Markov trajectories originating and terminating at a state as a measure of the stability of a state of a Markov process. These entropies can be computed in terms of the entropy rates and stationary…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of computational predictions of NMR chemical shieldings of candidate structures, which are usually taken to be local minima…
We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that…
Entropy is a fundamental thermodynamic quantity that is a measure of the accessible microstates available to a system, with the stability of a system determined by the magnitude of the total entropy of the system. This is valid across truly…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
The reduced density matrix that characterises the state of an open quantum system is a projection from the full density matrix of the quantum system and its environment, and there are many full density matrices consistent with a given…
We present a theory of the entanglement transition tuned by measurement strength in qudit chains evolved by random unitary circuits and subject to either weak or random projective measurements. The transition can be understood as a…
We explore the effects of spatial locality on the dynamics of random quantum systems subject to a Markovian noise. To this end, we study a model in which the system Hamiltonian and its couplings to the noise are random matrices whose…
Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
The dynamics of 3He atoms in solid 4He have been investigated by measuring the NMR relaxation times T1, T2 in the region where a significant non-classical rotational inertia fraction (NCRIF) has been reported. For 3He concentrations x3 = 16…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step…
The development of ferromagnetism in Mn-doped Bi2Te3 is characterized through measurements on a series of single crystals with different Mn content. Scanning tunneling microscopy analysis shows that the Mn substitutes on the Bi sites,…
This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads…