arXiv subjects

B. K. Clark

Publications and source records attributed to B. K. Clark.

4 recordsLinked to original sources

arXiv2022

Thermodynamics of chromosome inversions and 100 million years of Lachancea evolution

Gene sequences of a deme evolve over time as new chromosome inversions appear in a population via mutations, some of which will replace an existing sequence. The underlying biochemical processes that generates these and other mutations are governed by the laws of thermodynamics, although the connection between thermodynamics and the generation and propagation of mutations are often neglected. Here, chromosome inversions are modeled as a specific example of mutations in an evolving system. The thermodynamic concepts of chemical potential, energy, and temperature are linked to the input parameters that include inversion rate, recombination loss rate and deme size. An energy barrier to existing gene sequence replacement is a natural consequence of the model. Finally, the model calculations are compared to the observed chromosome inversion distribution of the Lachancea genus of yeast. The model introduced in this work should be applicable to other types of mutations in evolving systems.

physics.bio-ph↗

arXiv2019

Deviation from the dipole-ice model in the new spinel spin-ice candidate, MgEr$_2$Se$_4$

In spin ice research, small variations in structure or interactions drive a multitude of different behaviors, yet the collection of known materials relies heavily on the `227' pyrochlore structure. Here, we present thermodynamic, structural and inelastic neutron scattering data on a new spin-ice material, MgEr$_2$Se$_4$, which contributes to the relatively under-explored family of rare-earth spinel chalcogenides. X-ray and neutron diffraction confirm a normal spinel structure, and places Er$^{3+}$ moments on an ideal pyrochlore sublattice. Measurement of crystal electric field excitations with inelastic neutron scattering confirms that the moments have perfect Ising character, and further identifies the ground state Kramers doublet as having dipolar-octupolar form with a significant multipolar character. Heat capacity and magnetic neutron diffuse scattering have ice-like features, but are inconsistent with Monte Carlo simulations of the nearest-neighbor and next-nearest-neighbor dipolar spin-ice (DSI) models. A significant remnant entropy is observed as $T\rightarrow0$~K, but again falls short of the full Pauling expectation for DSI, unless significant disorder is added. We show that these observations are fully in-line with what is recently reported for CdEr$_2$Se$_4$, and point to the importance of quantum fluctuations in these materials.

cond-mat.dis-nn↗

arXiv2013

Multi-Determinant Wave-functions in Quantum Monte Carlo

Quantum Monte Carlo (QMC) methods have received considerable attention over the last decades due to their great promise for providing a direct solution to the many-body Schrodinger equation in electronic systems. Thanks to their low scaling with number of particles, QMC methods present a compelling competitive alternative for the accurate study of large molecular systems and solid state calculations. In spite of such promise, the method has not permeated the quantum chemistry community broadly, mainly because of the fixed-node error, which can be large and whose control is difficult. In this Perspective, we present a systematic application of large scale multi-determinant expansions in QMC, and report on its impressive performance with first row dimers and the 55 molecules of the G1 test set. We demonstrate the potential of this strategy for systematically reducing the fixed-node error in the wave function and for achieving chemical accuracy in energy predictions. When compared to traditional quantum chemistry methods like MP2, CCSD(T), and various DFT approximations, the QMC results show a marked improvement over all of them. In fact, only the explicitly-correlated CCSD(T) method with a large basis set produces more accurate results. Further developments in trial wave functions and algorithmic improvements appear promising for rendering QMC as the benchmark standard in large electronic systems.

physics.chem-ph↗

arXiv2010

Nature of the spin liquid state of the Hubbard model on honeycomb lattice

Recent numerical work (Nature 464, 847 (2010)) indicates the existence of a spin liquid phase (SL) that intervenes between the antiferromagnetic and semimetallic phases of the half filled Hubbard model on a honeycomb lattice. To better understand the nature of this exotic phase, we study the quantum $J_1-J_2$ spin model on the honeycomb lattice, which provides an effective description of the Mott insulating region of the Hubbard model. Employing the variational Monte Carlo approach, we analyze the phase diagram of the model, finding a phase transition between antiferromagnet and an unusual $Z_2$ SL state at $J_2/J_1\approx 0.08$, which we identify as the SL phase of the Hubbard model. At higher $J_2/J_1\gtrsim 0.3$ we find a transition to a dimerized state with spontaneously broken rotational symmetry.

cond-mat.str-el↗