相关论文: Universality of fold-encoded localized vibrations …

Projective measurement, a basic operation in quantum mechanics, can induce seemingly nonlocal effects. In this work, we analyze such effects in many-body systems by studying the non-equilibrium dynamics of weakly monitored quantum circuits,…

Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is…

We show how to speed up global optimization of molecular structures using machine learning methods. To represent the molecular structures we introduce the auto-bag feature vector that combines: i) a local feature vector for each atom, ii)…

A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon,…

Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…

Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…

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…

In collider experiments, an event is characterized by two distinct yet mutually complementary features: the `global features' and the `local features'. Kinematic information such as the event topology of a hard process, masses, and spins of…

Biochemical reactions typically occur at low copy numbers, but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a…

The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…

One approach to quantifying biological diversity consists of characterizing the statistical distribution of specific properties of a taxonomic group or habitat. Microorganisms living in fluid environments, and for whom motility is key,…

Cavity dressing of molecular vibrational dynamics expands the role of characteristic vibrations as spectroscopic markers of underlying ultrafast dynamics. Interacting vibrational modes exhibit a pronounced excited state delocalization due…

Physical kinetic roughening processes are well known to exhibit universal scaling of observables that fluctuate in space and time. Are there analogous dynamic scaling laws that are unique to the chemical reaction mechanisms available…

The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The…

A general theory of electronic excitations in aggregates of molecules coupled to intramolecular vibrations and the harmonic environment is developed for simulation of the third-order nonlinear spectroscopy signals. The model is applied in…

Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive…

Classical tools of nonlinear dynamics are used to study the highly excited vibrations of small molecules. For effective Hamiltonians with one polyad number (approximate constant of motion), previously developed methods locate new anharmonic…

A simple model to predict the directionality of vibrational energy flow at molecular level is presented. This model is based on a vibrational energy propagation analysis using ab intio molecular dynamics and the Fukui function and local…

A numerical simulation of vibrational excitation of molecules was devised, and used to excite computational models of common molecules into a prescribed, pure, normal vibration mode in the ground electronic state, with varying, controlable…