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We introduce Cryoscope, a method for sampling on-chip baseband pulses used to dynamically control qubit frequency in a quantum processor. We specifically use Cryoscope to measure the step response of the dedicated flux control lines of…
We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nos'e-Poincar'e thermostat, recently developed by Bond, Leimkuhler and Laird…
Computational Fluid Dynamics (CFD) is currently used to design and improve the hydraulic properties of biomedical devices, wherein the large scale blood circulation needs to be simulated by accounting for the mechanical response of red…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…
First-principles prediction of lattice thermal conductivity $\kappa_L$ of strongly anharmonic crystals is a long-standing challenge in solid state physics. Making use of recent advances in information science, we propose a systematic and…
We performed molecular dynamics simulations to investigate the viscoelastic properties of aqueous protein solutions containing an antifreeze protein, a toxin protein, and bovine serum albumin. These simulations covered a temperature range…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
We update the capabilities of the open-knowledge software instrument Modules for Experiments in Stellar Astrophysics (MESA). RSP is a new functionality in MESAstar that models the non-linear radial stellar pulsations that characterize RR…
Data on temperature-dependent, anisotropic thermal expansion in pure and doped RAgSb2 (R = Y, Sm, La) single crystals are presented. Using the Ehrenfest relation and heat capacity measurements, uniaxial pressure derivatives for long range…
Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy…
We present here two novel algorithms for simulated tempering simulations, which break detailed balance condition (DBC) but satisfy the skewed detailed balance to ensure invariance of the target distribution. The irreversible methods we…
We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment --- simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by 4 million…
Quantifying the temperature of microdevices is critical for probing nanoscale energy transport.Such quantification is often accomplished by integrating resistance thermometers into microdevices. However, such thermometers frequently become…
Molecular dynamics simulations are used to model ion and neutral temperature evolution in partially-ionized atmospheric pressure plasma at different ionization fractions. Results show that ion-ion interactions are strongly coupled at…
Restricted Boltzmann Machines (RBMs) are typically trained using finite-length Gibbs chains under a fixed sampling temperature. This practice implicitly assumes that the stochastic regime remains valid as the energy landscape evolves during…
Understanding relaxation processes is an important unsolved problem in many areas of physics. A key challenge in studying such non-equilibrium dynamics is the scarcity of experimental tools for characterizing their complex transient states.…
While recent advances have established efficient quantum algorithms for preparing Gibbs states of finite-dimensional systems, comparable complexity results for bosonic and other infinite-dimensional models remain unexplored. We introduce…