Related papers: A Proposal on Quantum Histone Modification in Gene…
We study the dynamics of a first-order phase transition in a strongly coupled gauge theory at non-zero temperature and chemical potential, computing nucleation rates and wall speeds from first principles. The gauge theory is the…
In a short article submitted to ArXiv [1], Maddamsetti et al. argue that the variation in the neutral mutation rate among genes in Escherichia coli that we recently reported [2] might be explained by horizontal gene transfer (HGT). To…
In this paper, we develop a method for obtaining the approximate solution for the evolution of single-step transformations under non-isothermal conditions. We have applied it to many reaction models and obtained very simple analytical…
A quasi-static process is realized in a purely quantum-mechanical model which is described by oscillator (or particle) systems having relative-phase interactions. Time development of a mixture of two oscillator (or particle) systems which…
In adiabatic quantum computing the aim is to track an eigenstate as the Hamiltonian changes. In the usual setup this is achieved using the natural time-dependent Hamiltonian evolution of the system and the main technical tool is the…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
We propose a modification of the embedded-atom method-type potential aiming at reconciling simulated melting and ground-state properties of metals by means of classical molecular dynamics. Considering titanium, magnesium, gold, and platinum…
As quantum computers become real, it is high time we come up with effective techniques that help programmers write correct quantum programs. Inspired by Hoare Type Theory in classical computing, we propose Quantum Hoare Type Theory (QHTT),…
We investigate whether making the friction spatially dependent on the reaction coordinate introduces quantum effects into the thermal reaction rates for dissipative reactions. Quantum rates are calculated using the numerically exact…
The smallness of the variation rate of the hamiltonian matrix elements compared to the (square of the) energy spectrum gap is usually believed to be the key parameter for a quantum adiabatic evolution. However it is only perturbatively…
Computational methods are needed to differentiate the small fraction of missense mutations that contribute to disease by disrupting protein function from neutral variants. We describe several complementary methods using large-scale homology…
The development of substrates with a switchable wettability is on a fast pace. The limit of switching frequencies and contact angle differences between substrate states are steadily pushed further. We investigate the behavior of a droplet…
The Stone theorem requires that in a physical Hilbert space ${\cal H}$ the time-evolution of a stable quantum system is unitary if and only if the corresponding Hamiltonian $H$ is self-adjoint. Sometimes, a simpler picture of the evolution…
We use the time-independent quantum-mechanical formulation of reactive collisions in order to investigate the state-to-state $\mathrm{H}^+ + \mathrm{HD} \to \mathrm{D}^+ + \mathrm{H}_2$ chemical reaction. We compute cross sections for…
Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
We study the transition probabilities of a two-point measurement on a quantum system, initially prepared in a thermal state. We find two independent constraints on the difference between transition probabilities when the system is prepared…
Temperature determines the relative probability of observing a physical system in an energy state when that system is energetically in equilibrium with its environment. In this paper, we present a theory for engineering the temperature of a…
The temperature dependence of the response of a magnetic system to an applied field can be understood qualitatively by considering variations in the energy surface characterizing the system and estimated quantitatively with rate theory. In…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…