Related papers: Enzyme as a thermal resonance pump
Chaotic lattice models at high temperature are generically expected to exhibit diffusive transport of all local conserved charges. Such diffusive transport is usually associated with overdamped relaxation of the associated currents. Here we…
Using fully kinetic Particle In Cell simulations, we investigate the stability and performance of autoresonant plasma beat wave excitation in plasmas with tailored density profiles. We show that a prescribed spatial variation of the…
The Feynman-Vernon path integral formalism is used to derive the density matrix of a quantum oscillator that is linearly coupled to an environmental reservoir. Although low-temperature reservoirs thermalize the oscillator to the usual…
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations,…
Recently a formulation of overlap fermions at finite density based on an analytic continuation of the sign function was proposed. We study this proposal by analyzing the energy and number densities for free fermions as a function of the…
Analyzing correlation functions of charmonia at finite temperature ($T$) on $32^3\times(32-96)$ anisotropic lattices by the maximum entropy method (MEM), we find that $J/\psi$ and $\eta_c$ survive as distinct resonances in the plasma even…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
Variational quantum algorithms offer a promising framework for solving eigenvalue problems on near-term quantum hardware, yet their applicability beyond electronic structure calculations remains relatively unexplored. In this work, we…
Only about 1,000 qualitatively different protein folds are believed to exist in nature. Here, we review theoretical studies which suggest that some folds are intrinsically more designable than others, {\it i.e.} are lowest energy states of…
The interaction energies between the different types of bases of a single strand of DNA molecule have been calculated. Using these original values of energies the harmonic behavior of a number of base patterns of DNA has been studied. In…
Protein structure tokenizers (PSTs) are workhorses in protein language modeling, function prediction, and evolutionary analysis. However, existing PSTs only capture local geometry of static structures, and miss the correlated motions and…
We introduce a simplified protein model where the water degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover both the warm and the cold protein denaturation within a…
This is a Review of experimental observations and theoretical developments on the c-axis plasma oscillations in High-temperature superconductors.
Periodic phenomena are oscillating signals found in many naturally-occurring time series. A periodogram can be used to measure the intensities of oscillations at different frequencies over an entire time series but sometimes we are…
Boolean network models of strongly connected modules are capable of capturing the high regulatory complexity of many biological gene regulatory circuits. We study numerically the previously introduced basin entropy, a parameter for the…
Representing an ensemble of random lasers with an ensemble of random matrices, we compute average number of lasing modes and its fluctuations. The regimes of weak and strong coupling of the passive resonator to environment are considered.…
Mounting evidence shows that oscillatory activity is widespread in cell signaling. Here we review some of this recent evidence, focusing on both the molecular mechanisms that potentially underlie such dynamical behavior, and the potential…
Developing enzymes with desired thermal properties is crucial for a wide range of industrial and research applications, and determining temperature stability is an essential step in this process. Experimental determination of thermal…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…
Infrared pump-probe spectroscopy provides detailed information on the dynamics of hydrogen-bonded liquids. Due to dissipation of the absorbed pump pulse energy, also thermal equilibration dynamics contributes to the observed signal.…