A5000128828- Spectroscopy and Quantum Chemical Studies
- Machine Learning in Materials Science
- Protein Structure and Dynamics
- Advanced Chemical Physics Studies
- Genetics, Bioinformatics, and Biomedical Research
- Various Chemistry Research Topics
- Quantum, superfluid, helium dynamics
- Gene Regulatory Network Analysis
- Thermodynamic properties of mixtures
- Chemical and Physical Properties in Aqueous Solutions
- Consumer Attitudes and Food Labeling
- Quantum many-body systems
- Obesity, Physical Activity, Diet
- Microbial Metabolic Engineering and Bioproduction
- Advanced NMR Techniques and Applications
- E-Learning and Knowledge Management
- Single-cell and spatial transcriptomics
- Electrochemical Analysis and Applications
- Mass Spectrometry Techniques and Applications
- Biochemical Analysis and Sensing Techniques
- Cell Image Analysis Techniques
- Boron and Carbon Nanomaterials Research
- NMR spectroscopy and applications
- Culinary Culture and Tourism
- Biomedical and Engineering Education
University of California, San Diego
2022-2025
St. John's School
2024
Saint Joseph Seminary College
2024
College of Saint Benedict and Saint John's University
2024
Yale University
2009
We assessed the impact of restaurant menu calorie labels on food choices and intake.Participants in a study dinner (n=303) were randomly assigned to either (1) without (no labels), (2) with (calorie or (3) label stating recommended daily caloric intake for an average adult plus information). Food during after measured.Participants both conditions ordered fewer calories than those no condition. When combined, that group consumed 14% group. Individuals condition more other conditions....
Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of interactions to achieve chemical accuracy from gas condensed phases. MBX can be employed either as stand-alone package or energy/force engine integrated generic software for molecular dynamics and Monte Carlo simulations. parallelized...
In this study, we explore the impact of alkali metal ions (Li+, Na+, K+, Rb+, and Cs+) on hydration structure water using molecular dynamics simulations carried out with MB-nrg potential energy functions (PEFs). Our analyses include radial distribution functions, coordination numbers, dipole moments, infrared spectra molecules, calculated as a function solvation shells. The results collectively indicate highly local influence all hydrogen-bond network established by surrounding smallest most...
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging reproduce reuse simulations, in part, because the numerous formats methods for simulating various subsystems scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find use simulation tools, we developed BioSimulators (https://biosimulators.org), central registry of capabilities...
In this observational study, we determined how frequently consumers accessed on-premises nutrition information provided at chain restaurants. The number of patrons entering and accessing was recorded 8 locations that were part 4 major restaurant chains (McDonald's, Burger King, Starbucks, Au Bon Pain). Only 6 (0.1%) 4311 before purchasing food. This very small percentage suggests such should be more prominently displayed, as on menu boards, to help customers make informed decisions.
The structure and dynamics of water at charged graphene interfaces fundamentally influence molecular responses to electric fields with implications for applications in energy storage, catalysis, surface chemistry. Leveraging the realism MB-pol data-driven many-body potential advanced path-integral quantum dynamics, we analyze vibrational sum frequency generation (vSFG) spectrum graphene/water under varying charges. Our simulations reveal a distinctive dangling OH peak vSFG neutral graphene,...
The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these functions integrate physics-based machine-learned terms trained on electronic structure data calculated at ``gold standard'' coupled cluster level of theory. Recent advancements in have focused optimizing its performance, resulting release v1.2. While inherently nature ensures...
The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these functions integrate physics-based machine-learned terms trained on electronic structure data calculated at "gold standard" coupled-cluster level of theory. Recent advancements in have focused optimizing its performance, resulting release v1.2. While inherently nature ensures...
Understanding how halide ions affect the structure and dynamics of water at molecular level is essential for a wide range chemical, biological, environmental processes. In this study, we use simulations with MB-nrg data-driven many-body potential energy functions to investigate hydration properties in bulk water. The results reveal distinct trends structure, residence times, dipole moment distributions, infrared spectral signatures, reflecting variations ion size, charge density,...
In this study, we explore the impact of alkali metal ions (Li+, Na+, K+, Rb+, and Cs+) on hydration structure water using molecular dynamics simulations carried out with MB-nrg potential energy functions (PEFs). Our analyses include radial distribution functions, coordination numbers, dipole moments, infrared spectra molecules, calculated as a function solvation shells. The results collectively indicate highly local influence all hydrogen-bond network established by surrounding smallest most...
Developing a molecular-level understanding of the properties water is central to numerous scientific and technological applications. However, accurately modeling through computer simulations has been significant challenge due complex nature hydrogen- bonding network that molecules form under different thermodynamic conditions. This complexity led over five decades research many attempts. The introduction MB-pol data-driven many-body potential energy function marked advancement toward...
We are developing a new fee online biochemistry text, Fundamentals of Biochemistry, within the LibreTexts project (Libretexts.org) as part Department Education funded grant to produce textbooks for all chemistry courses required four-year ACS certified degree. This text covers full year sequence and will be available in Fall 2022. The book could serve traditional, ASBMB-certified ACS-certified majors, well students taking one-semester course. Adopting instructors create custom from content....
MBX is a C++ library that implements many-body potential energy functions (PEFs) within the “many-body energy” (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of interactions to achieve chemical accuracy from gas condensed phases. can be employed either as stand-alone package or energy/force engine integrated generic software for molecular dynamics and Monte Carlo simulations. parallelized internally using OpenMP,...
In this study, we explore the impact of alkali metal ions (Li+, Na+, K+, Rb+, and Cs+) on hydration structure water using molecular dynamics simulations carried out with MB-nrg potential energy functions (PEFs). Our analyses include radial distribution functions, coordination numbers, dipole moments, infrared spectra molecules, calculated as a function solvation shells. The results collectively indicate highly local influence all hydrogen-bond network established by surrounding smallest most...
Abstract Biology is perhaps the most complex of sciences, given incredible variety chemical species that are interconnected in spatial and temporal pathways daunting to understand. Their interconnections lead emergent properties such as memory, consciousness, recognition self non‐self. To understand how these reactions cellular life characterized by activation, inhibition, regulation, homeostasis, adaptation, computational analyses simulations essential, a fact recognized biological...
Developing a molecular-level understanding of the properties water is central to numerous scientific and technological applications. However, accurately modeling through computer simulations has been significant challenge due complex nature hydrogen- bonding network that molecules form under different thermodynamic conditions. This complexity led over five decades research many attempts. The introduction MB-pol data-driven many-body potential energy function marked advancement toward...
The structure and dynamics of water at charged graphene interfaces fundamentally influence molecular responses to electric fields, with implications for applications in energy storage, catalysis, surface chemistry. Leveraging the realism MB-pol data-driven many-body potential advanced path-integral quantum dynamics, we analyze vibrational sum-frequency generation (vSFG) spectrum graphene/water under varying charges. Our simulations reveal a distinctive dangling OH peak vSFG neutral graphene,...
The MBX software provides an interface to perform molecular dynamics simulations using the MB-pol water model and other MB-nrg potential energy functions. These PEFs, developed over last decade, combine a long-range physically-inspired baseline with short-range data-driven many-body permutationally invariant polynomials trained electronic structure data in order achieve near ab initio accuracy at fraction of cost. Recently, performance has become focus its development significant progress...
The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these functions integrate physics-based machine-learned terms trained on electronic structure data calculated at ``gold standard'' coupled cluster level of theory. Recent advancements in have focused optimizing its performance, resulting release v1.2. While inherently nature ensures...
Enzyme kinetics is challenging for students to understand and apply. Why? Perhaps it's because we teach it in isolation rarely revisit a class or throughout the biology chemistry curricula. It also requires integrate mathematical, structural, mechanistic understandings, tall order requiring cognitive processing multiple fields. Students generally conservation of mass, length, volume by about age 11, but derivative quantities take longer. Examples include density (m/V, 15) both concentration...
Biology is perhaps the most complex of sciences, given incredible variety chemical species that are interconnected in spatial and temporal pathways daunting to understand. Their interconnections lead emergent properties such as memory, consciousness, recognition self non-self. To understand how these reactions cellular life characterized by activation, inhibition, regulation, homeostasis, adaptation, computational analyses simulations essential, a fact recognized biological communities. At...
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging reproduce reuse simulations, in part, because the numerous formats methods for simulating various subsystems scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find use simulation tools, we developed BioSimulators (https://biosimulators.org), central registry of capabilities...