Related papers: Nonequilibrium effects in DNA microarrays: a multi…
This paper describes the effects of electronic nonequilibrium in a simulation of ultrafast laser irradiation of materials. The simulation scheme based on tight-binding molecular dynamics, in which the electronic populations are traced with…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
We calibrate a (3+1)-dimensional multistage hybrid framework using the measured pseudo-rapidity distribution of charged particles and rapidity distribution of net protons for central Au+Au collisions at $\sqrt{s_{\rm…
In this paper we report direct measurement of large low frequency temperature fluctuations in double stranded (ds) DNA when it undergoes thermal denaturation transition. The fluctuation, which occurs only in the temperature range where the…
The present study addresses the role of molecular non-equilibrium effects in thermal ignition problems. We consider a single binary reaction of the form A+B -> C+C. Molecular dynamics calculations were performed for activation energies…
The integrable system is constrained strictly by the conservation law during the time evolution, and the nearly integrable system or nonintegrable system is also constrained by the conserved parameters (like the constants of motion) with…
Closely related to the laws of thermodynamics, the detection and quantification of disequilibria are crucial in unraveling the complexities of nature, particularly those beneath observable layers. Theoretical developments in nonequilibrium…
Characterizing and optimizing thermodynamic processes far from equilibrium is a challenge. This is especially true for nanoscopic systems made of few particles. We here theoretically and experimentally investigate the nonequilibrium…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Recent laboratory experiments suggest an intrinsic asymmetry between heating and cooling, with heating occurring more efficiently. Two decades earlier, molecular dynamics (MD) simulations had examined a related setup - heating one side of a…
Interest in studying the interaction of small molecules with DNA is caused by the need to develop new, highly effective, and low-toxic drugs for cancer treatment. The strong and highly specific binding of thionine with DNA makes it a…
State-of-the-art simulations of high-energy nuclear collisions rely on hybrid setups, involving in particular a pre-equilibrium stage to let the system evolve from a far-from-equilibrium initial condition towards a near-equilibrated state…
Ehrenfest urns with interaction that are connected in a ring is considered as a paradigm model for non-equilibrium thermodynamics and is shown to exhibit two distinct non-equilibrium steady states (NESS) of uniform and non-uniform particle…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
We review a series of experimental studies of the thermodynamics of nonequilibrium processes at the microscale. In particular, in these experiments we studied the fluctuations of the thermodynamic properties of a single optically-trapped…