Related papers: The dynamical transition in proteins and non-Gauss…
We investigate dynamic properties of inhomogeneous nano-materials, which appear in analytical descriptions typically as series of $\delta$-functions with corresponding Gibbs weights. We focus on observables relevant for transport theories…
We use molecular dynamics simulations to investigate dynamic heterogeneities and the potential energy landscape of the Gaussian core model (GCM). Despite the nearly Gaussian statistics of particles' displacements, the GCM exhibits giant…
The atomic motion in molecular crystals, such as high-pressure hydrogen or hybrid organic-inorganic perovskites, is very complex due to quantum anharmonic effects. In addition, these materials accommodate rotational degrees of freedom. All…
We have extended our analytically derived PDB-NMA formulation, ATMAN [1], to include protein dimers using mixed internal and Cartesian coordinates. A test case on a 1.3\AA\ resolution model of a small homodimer, ActVA-ORF6, consisting of…
Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
Driven non-equilibrium structural phase transformation has been probed using time varying resistance fluctuations or noise. We demonstrate that the non-Gaussian component (NGC) of noise obtained by evaluating the higher order statistics of…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
Novel physical mechanism is proposed for explanation of temperature-independent transition reactions in molecular systems. The mechanism becomes effective in the case of conformation transitions between quasi-isoenergetic molecular states.…
Combining elastic incoherent neutron scattering experiments at different resolutions with molecular dynamics simulations, we report the observation of a protein-like dynamical transition in linear chains of Poly(N-isopropylacrylamide). We…
The Self-Consistent Harmonic Approximation (SCHA) describes atoms in solids, including quantum fluctuations and anharmonic effects, in a non-perturbative way. It computes ionic free energy variationally, constraining the atomic…
In biological systems, expression dynamics that can provide fitted phenotype patterns with respect to a specific function have evolved through mutations. This has been observed in the evolution of proteins for realizing folding dynamics…
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…
Protein function prediction is dominated by representations grounded in sequence and static structure, neither of which captures the collective vibrational dynamics through which proteins act. Here we introduce frequency-space mechanics, a…
Phase transitions are fundamental in nature. A small parameter change near a critical point leads to a qualitative change in system properties. Across a regular phase transition, the system remains in thermal equilibrium and, therefore,…
The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
The protein dynamical transition is investigated as a function of protein structure using terahertz time domain spectroscopy (THz-TDS). Measurements performed for native state and denatured hen egg white lysozyme (HEWL) show that protein…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier, 1-parameter formulation (M. Tirion, PRL 77, 1905 (1996)) that characterized the slow modes associated with protein data bank…