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| Open AccessTheoretical formulation of chemical equilibrium under vibrational strong coupling
Strong light-matter interactions in optical microcavities can be used to control molecular kinetic and thermodynamic phenomena. Here, the authors introduce a theory that describes the nonperturbative effects of infrared microcavities on chemical equilibria.
- Kaihong Sun
- & Raphael F. Ribeiro
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| Open AccessRealistic phase diagram of water from “first principles” data-driven quantum simulations
The molecular modelling of water has been a long sought-after goal in computational sciences for more than 50 years. Here, the authors show that the data-driven many-body MB-pol potential can provide a realistic representation of the phase diagram of water.
- Sigbjørn Løland Bore
- & Francesco Paesani
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Article
| Open AccessProbing excitations and cooperatively rearranging regions in deeply supercooled liquids
Experimental data of the transition of a supercooled liquid into glass is compatible with both dynamic and thermodynamic theories. Here the authors use experiments and MD simulations at very low temperatures to show that both theories are connected.
- Levke Ortlieb
- , Trond S. Ingebrigtsen
- & C. Patrick Royall
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Article
| Open AccessPath sampling of recurrent neural networks by incorporating known physics
Adding prior experimentally or theoretically obtained knowledge to the training of recurrent neural networks may be challenging due to their feedback nature with arbitrarily long memories. The authors propose a path sampling approach that allows to include generic thermodynamic or kinetic constraints for learning of time series relevant to molecular dynamics and quantum systems.
- Sun-Ting Tsai
- , Eric Fields
- & Pratyush Tiwary
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| Open AccessAllotropy in ultra high strength materials
Here the authors propose a crystal thermodynamics framework describing the tensor stress induced phase transformations in solids based on nonlinear elasticity and first principles calculations. The proposed approach enables balanced design of high-strength, high-ductility materials.
- A. S. L. Subrahmanyam Pattamatta
- & David J. Srolovitz
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Article
| Open AccessSimulating a chemically fueled molecular motor with nonequilibrium molecular dynamics
Molecular motors move in response to an imbalance between concentrations of fuel and waste molecules. Here, the authors simulate such non-equilibrium conditions to characterize a model motor’s performance and mechanism of operation.
- Alex Albaugh
- & Todd R. Gingrich
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Article
| Open AccessUptake of N2O5 by aqueous aerosol unveiled using chemically accurate many-body potentials
The reactive uptake of N2O5 to aqueous aerosol is a major loss channel for nitrogen oxides in the troposphere. Here authors report a theoretical investigation on the N2O5 uptake into aqueous aerosol and determine the hydrolysis rates by numerically solving a molecularly detailed reaction–diffusion equation.
- Vinícius Wilian D. Cruzeiro
- , Mirza Galib
- & Andreas W. Götz
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Article
| Open AccessA general theoretical framework to design base editors with reduced bystander effects
Base editors can edit target nucleotides, and identical ones that are within the editing window. Here the authors build an analytical model to propose general principles of editor design to reduce bystander effects.
- Qian Wang
- , Jie Yang
- & Anatoly B. Kolomeisky
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| Open AccessQuantum-mechanical exploration of the phase diagram of water
Complex interatomic interactions and diverse structures make computing the phase diagram of water very challenging. Here, a combination of machine learning and advanced free-energy methods at three levels of hybrid DFT enables the prediction of the phase diagram in close agreement with experiment.
- Aleks Reinhardt
- & Bingqing Cheng
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Article
| Open AccessTRIM5α self-assembly and compartmentalization of the HIV-1 viral capsid
Tripartite-motif containing (TRIM) proteins modulate cellular responses to viral infection. Here the authors use molecular dynamics simulations to demonstrate that TRIM5α uses a two-dimensional lattice hopping mechanism to aggregate on the HIV capsid surface and initiate lattice growth.
- Alvin Yu
- , Katarzyna A. Skorupka
- & Gregory A. Voth
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Article
| Open AccessHydrogen bonding structure of confined water templated by a metal-organic framework with open metal sites
The properties of water under confinement are significantly altered with respect to the bulk phase. Here the authors use infrared spectroscopy and many-body molecular dynamics simulations to show the structure and dynamics of confined water as a function of relative humidity within a metal-organic framework.
- Adam J. Rieth
- , Kelly M. Hunter
- & Francesco Paesani
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Article
| Open AccessThe Chemical Fluctuation Theorem governing gene expression
A unified framework to understand gene expression noise is still lacking. Here the authors derive a universal theorem relating the biological noise with dynamics of birth and death processes and present a model of transcription dynamics, allowing analytical prediction of the dependence of mRNA noise on mRNA lifetime variability.
- Seong Jun Park
- , Sanggeun Song
- & Jaeyoung Sung
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Article
| Open AccessThe role of fivefold symmetry in suppressing crystallization
The suppression of crystallization due to the appearance of structures with fivefold symmetry is widely adopted, but its kinetic and thermodynamic origin remains elusive. Taffs et al.show that fivefold symmetry substantially slows down the nucleation rate but not the crystal growth rate as expected.
- Jade Taffs
- & C. Patrick Royall
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Binary colloidal structures assembled through Ising interactions
The assembly of microscopic particles into macroscopic structures may allow the fabrication of complex materials, but general strategies to provide a wide variety of structures are lacking. Khalilet al. develop a colloidal assembly system, which can be tuned to provide over 20 different pre-programmed structures.
- Karim S. Khalil
- , Amanda Sagastegui
- & Benjamin B. Yellen
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Size and mechanics effects in surface-induced melting of nanoparticles
Melting-related phenomena are of fundamental and applied interest, but the melting theory is poorly understood. Levitas and Samani develop an advanced phase-field theory of melting coupled to mechanics that resolves existing contradictions and reveals the features of melting phenomena.
- Valery I Levitas
- & Kamran Samani