A5036947439- Advanced Chemical Physics Studies
- Physics of Superconductivity and Magnetism
- Cold Atom Physics and Bose-Einstein Condensates
- Quantum, superfluid, helium dynamics
- Machine Learning in Materials Science
- Advanced biosensing and bioanalysis techniques
- Quantum many-body systems
- DNA and Biological Computing
- Protein Structure and Dynamics
- Quantum and electron transport phenomena
- Advanced Condensed Matter Physics
- 2D Materials and Applications
- RNA and protein synthesis mechanisms
- Quantum Computing Algorithms and Architecture
- Computational Drug Discovery Methods
- Catalysis and Oxidation Reactions
- Advanced Thermodynamics and Statistical Mechanics
- Magnetic and transport properties of perovskites and related materials
- Theoretical and Computational Physics
- Innovative Microfluidic and Catalytic Techniques Innovation
- Quantum Information and Cryptography
- Catalytic Processes in Materials Science
- Spectroscopy and Quantum Chemical Studies
- Machine Learning in Bioinformatics
- Chronic Myeloid Leukemia Treatments
John Brown University
2020-2025
Brown University
2016-2025
Providence College
2021-2024
Quantum Simulations (United States)
2016-2019
Lawrence Livermore National Laboratory
2016-2019
Columbia University
2008-2012
QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, some model Hamiltonians. Implemented real space algorithms include variational, diffusion, reptation Carlo. uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable optimizing tens thousands parameters. The orbital auxiliary-field method also implemented, enabling cross...
Abstract This paper presents an innovative approach for predicting the relative populations of protein conformations using AlphaFold 2, AI-powered method that has revolutionized biology by enabling accurate prediction structures. While 2 shown exceptional accuracy and speed, it is designed to predict proteins’ ground state limited in its ability conformational landscapes. Here, we demonstrate how can directly different subsampling multiple sequence alignments. We tested our against nuclear...
We review recent advances in the capabilities of open source ab initio Quantum Monte Carlo (QMC) package QMCPACK and workflow tool Nexus used for greater efficiency reproducibility. The auxiliary field QMC (AFQMC) implementation has been greatly expanded to include k-point symmetries, tensor-hypercontraction, accelerated graphical processing unit (GPU) support. These scaling memory reductions increase number orbitals that can practically be included AFQMC calculations, increasing accuracy....
Doped lead halide perovskite nanocrystals (NCs) have garnered significant attention due to their superior optoelectronic properties. Here, we report a synthesis of Cd-doped CsPbCl3 NCs by decoupling Pb- and Cl-precursors in hot injection method. The resulting manifest dual-wavelength emission profile with the first reported example Cd-dopant emission. By controlling concentration, can be tuned dopant quantum yield up 8%. A new secondary (∼610 nm) is induced an energy transfer process from...
Formamidinium lead halide (FAPbX3, X = Cl, Br, I) perovskite materials have recently drawn an increased amount of attention owing to their superior optoelectronic properties and enhanced material stability as compared with methylammonium-based (MA-based) analogues. Herein, we report a study the pressure-induced structural optical evolutions FAPbI3 hybrid organic–inorganic nanocrystals (NCs) using synchrotron-based X-ray scattering technique coupled in situ absorption photoluminescence...
The relationship between the thermodynamic and computational properties of physical systems has been a major theoretical interest since at least 19th century. It also become increasing practical importance over last half-century as energetic cost digital devices exploded. Importantly, real-world computers obey multiple constraints on how they work, which affects their properties. Moreover, many these apply to both naturally occurring computers, like brains or Eukaryotic cells, systems. Most...
Multicomponent reactions enable the synthesis of large molecular libraries from relatively few inputs. This scalability has led to broad adoption these by pharmaceutical industry. Here, we employ four-component Ugi reaction demonstrate that multicomponent can provide a basis for large-scale data storage. Using this combinatorial chemistry encode more than 1.8 million bits art historical images, including Cubist drawing Picasso. Digital is written using robotically synthesized products, and...
Abstract The sustained interest in investigating magnetism the 2D limit of insulating antiferromagnets is driven by possibilities discovering, or engineering, novel magnetic phases through layer stacking. However, due to difficulty directly measuring interactions antiferromagnets, it not yet understood how intra , strongly correlated, materials can be modified proximity. Herein, impact reduced dimensionality model van der Waals antiferromagnet NiPS 3 explored electronic excitations...
We present an ab initio auxiliary field quantum Monte Carlo method for studying the electronic structure of molecules, solids, and model Hamiltonians at finite temperature. The algorithm marries phaseless known to produce high accuracy ground state energies molecules solids with its temperature variant, long used by condensed matter physicists Hamiltonian phase diagrams, yield a phaseless, method. demonstrate that produces internal within chemical exact diagonalization results across wide...
The first magnetic 2D material discovered, monolayer (ML) CrI3, is particularly fascinating due to its ground state ferromagnetism. However, because ML materials are difficult probe experimentally, much remains unresolved about CrI3's structural, electronic, and properties. Here, we leverage Density Functional Theory (DFT) high-accuracy Diffusion Monte Carlo (DMC) simulations predict lattice parameters, moments, spin-phonon spin-lattice coupling of CrI3. We exploit a recently developed...
Light-dependent protochlorophyllide oxidoreductase (LPOR) is a photocatalytic enzyme in the chlorophyll (Chl) biosynthetic pathway that underwent duplications angiosperms, resulting emergence of multiple isoforms across various plant species. The physiological roles these LPOR homologs remained unclear, so we selected six species with different number enzyme, having diverse phylogenetic backgrounds, and characterized their properties vitro. Our findings revealed vary affinity for reaction...
The intrinsic dynamics of most proteins are central to their function. Protein tyrosine kinases such as Abl1 undergo significant conformational changes that modulate activity in response different stimuli. These constitute a conserved mechanism for self-regulation dramatically impacts kinases’ affinities inhibitors. Few studies have attempted extensively sample the pathways and elucidate mechanisms underlie kinase inactivation. In large part, this is consequence steep energy barriers...
The intrinsic dynamics of most proteins are central to their function. Protein tyrosine kinases such as Abl1 undergo significant conformational changes that modulate activity in response different stimuli. These constitute a conserved mechanism for self-regulation dramatically impacts kinases’ affinities inhibitors. Few studies have attempted extensively sample the pathways and elucidate mechanisms underlie kinase inactivation. In large part, this is consequence steep energy barriers...
We report the observation of a $\ensuremath{\pi}$-type dipole-bound state ($\ensuremath{\pi}$-DBS) in cryogenically cooled deprotonated 9-anthrol molecular anions ($9{\mathrm{AT}}^{\ensuremath{-}}$) by resonant two-photon photoelectron imaging. A DBS is observed $191\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}1}$ (0.0237 eV) below detachment threshold, and existence $\ensuremath{\pi}$-DBS revealed distinct ($s+d$)-wave angular distribution. The stabilized large anisotropic in-plane...
Identifying structural differences among proteins can be a non-trivial task. When contrasting ensembles of protein structures obtained from molecular dynamics simulations, biologically-relevant features easily overshadowed by spurious fluctuations. Here, we present SINATRA Pro, computational pipeline designed to robustly identify topological between two sets structures. Algorithmically, Pro works first taking in the 3D atomic coordinates for each snapshot and summarizing them according their...
Abstract Acid-base reactions are ubiquitous, easy to prepare, and execute without sophisticated equipment. Acids bases also inherently complementary naturally map a universal representation of “0” “1.” Here, we propose how leverage acids, bases, their encode binary information perform processing based upon the majority negation operations. These operations form functionally complete set that use implement more complex computations such as digital circuits neural networks. We present building...
Abstract The exchange‐correlation (XC) functional in density theory is used to approximate multi‐electron interactions. A plethora of different functionals are available, but nearly all based on the hierarchy inputs commonly referred as “Jacob's ladder.” This paper introduces an approach construct XC with from convolutions arbitrary kernels electron density, providing a route move beyond Jacob's ladder. We derive variational derivative these functionals, showing consistency generalized...
Neutral molecules with sufficiently large dipole moments can bind electrons in diffuse nonvalence orbitals most of their charge density far from the nuclei, forming so-called dipole-bound anions. Because long-range correlation effects play an important role binding excess electron and overall energies are often only on order 10s–100s wave numbers, predictively modeling anions remains a challenge. Here, we demonstrate that quantum Monte Carlo methods accurately characterize molecular...
One of the long-standing holy grails molecular evolution has been ability to predict an organism's fitness directly from its genotype. With such predictive abilities in hand, researchers would be able more accurately forecast how organisms will evolve and proteins with novel functions could engineered, leading revolutionary advances medicine biotechnology. In this work, we assemble largest reported set experimental TEM-1 β-lactamase folding free energies use data conjunction previously...
Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of first experimental demonstrations this idea used DNA, but nature also uses a wide diversity smaller non-polymeric molecules preserve, process, and transmit information. In paper, we present general framework for quantifying chemical memory, which is not limited polymers extends mixtures all types. We show that theoretical limit molecular two orders magnitude...
This paper presents a novel approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling accurate prediction structures. While 2 shown exceptional accuracy and speed, it is designed to predict proteins' single ground state limited in its ability fold switching effects mutations on conformational landscapes. Here, we demonstrate how can directly different proteins even accurately changes those...
We present a quantum Monte Carlo (QMC) technique for calculating the exact finite-temperature properties of Bose-Fermi mixtures. The Auxiliary-Field Quantum (BF-AFQMC) algorithm combines two methods, AFQMC bosons and variant standard fermions, into one demonstrate accuracy our method by comparing its results Bose-Hubbard Bose-Fermi-Hubbard models against those produced using diagonalization small systems. Comparisons are also made with mean-field theory worm larger As is case most fermion...
Biomolecular information systems offer exciting potential advantages and opportunities to complement conventional semiconductor technologies. Much attention has been paid information-encoding polymers, but small molecules also play important roles in biochemical systems. Downstream from DNA, the metabolome is an information-rich molecular system with diverse chemical dimensions which could be harnessed for storage processing. As a proof of principle small-molecule postgenomic data storage,...
Many experimentally accessible, finite-sized interacting quantum systems are most appropriately described by the canonical ensemble of statistical mechanics. Conventional numerical simulation methods either approximate them as being coupled to a particle bath or use projective algorithms which may suffer from nonoptimal scaling with system size large algorithmic prefactors. In this paper, we introduce highly stable, recursive auxiliary field Monte Carlo approach that can directly simulate in...