☆ 4.7 Article

Optimization of non-equilibrium self-assembly protocols using Markov state models

JOURNAL OF CHEMICAL PHYSICS (2022)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Computer Science, Interdisciplinary Applications

Optimal control of PDEs using physics-informed neural networks

Saviz Mowlavi et al.

Summary: Physics-informed neural networks (PINNs) are a popular method for solving forward and inverse problems governed by partial differential equations (PDEs). In this study, the PINN framework is extended to PDE-constrained optimal control problems. Guidelines are provided for obtaining a good optimal control solution using a suitable PINN architecture and training parameters, as well as a two-step line search strategy. The performance of the PINN framework is validated by comparing it to adjoint-based nonlinear optimal control on various distributed control examples based on different equations.

JOURNAL OF COMPUTATIONAL PHYSICS (2023)

添加到收藏夹

Article Multidisciplinary Sciences

Temperature protocols to guide selective self-assembly of competing structures

Arunkumar Bupathy et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

添加到收藏夹

Article Chemistry, Physical

GraphVAMPNet, using graph neural networks and variational approach to Markov processes for dynamical modeling of biomolecules

Mahdi Ghorbani et al.

Summary: This paper combines VAMPNet and graph neural networks to generate an end-to-end framework for efficiently learning high-level dynamics and metastable states from long-timescale molecular dynamics trajectories. The method combines the advantages of graph representation learning and VAMPNet, resulting in a higher resolution and more interpretable Markov model.

JOURNAL OF CHEMICAL PHYSICS (2022)

添加到收藏夹

Article Chemistry, Physical

Physics-informed graph neural networks enhance scalability of variational nonequilibrium optimal control

Jiawei Yan et al.

Summary: In nonequilibrium statistical mechanics, the statistical distribution of dynamical observables provides information about the physical properties of a system driven away from equilibrium. However, for complex, interacting systems, analytical calculation is often not feasible, therefore robust numerical techniques are needed. In this article, an algorithm based on optimal control problem is proposed, and the optimal control forces are solved using neural network ansatz tailored to the physical systems, which leads to transferable and accurate solutions in two systems with large numbers of interacting particles.

JOURNAL OF CHEMICAL PHYSICS (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Evolved interactions stabilize many coexisting phases in multicomponent liquids

David Zwicker et al.

Summary: Phase separation is an important concept for spatial organization in biological cells, but little is known about the phases formed in systems with many interacting components. Researchers have developed a numerical method based on physical relaxation dynamics to study coexisting phases in such systems. By optimizing interactions between components, similar to how proteins' interactions might have evolved, they found that these evolved interactions robustly lead to a defined number of phases and provide versatile control of phase behavior.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Self-assembly of emulsion droplets through programmable folding

Angus McMullen et al.

Summary: By programming the interactions of colloidal droplet chains, specific geometric structures can be achieved through self-folding.

NATURE (2022)

添加到收藏夹

Article Chemistry, Physical

Nonequilibrium self-assembly of multiple stored targets in a dimer-based system

Adi Ben-Ari et al.

Summary: Researchers used Monte Carlo simulations to study how certain factors such as initial seed size, interaction energy, and chemical potential affect the restoration of target structures in nonequilibrium self-assembly, as well as how nonequilibrium driving can overcome equilibrium constraints to achieve target assembly stability.

JOURNAL OF CHEMICAL PHYSICS (2021)

添加到收藏夹

Article Chemistry, Physical

What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models

Ernesto Suarez et al.

Summary: Markov state models (MSMs) are widely used in studying protein conformational dynamics, accurately reproducing correlation functions for states with longer lifetimes but facing stricter requirements for path-based observables; history-augmented MSMs (haMSMs) show more reliable performance in reproducing path-based observables, even in the presence of short-lived states.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

添加到收藏夹

Article Engineering, Electrical & Electronic

On-chip micro pressure sensor for microfluidic pressure monitoring

Renchang Zhang et al.

Summary: A novel on-chip micro pressure sensor was developed for microfluidic pressure monitoring, which can monitor the pressure of the working fluid by measuring the interface displacement of two immiscible fluids in the detection channel. It has the advantages of avoiding cross-contamination, low cost, and easy integration.

JOURNAL OF MICROMECHANICS AND MICROENGINEERING (2021)

添加到收藏夹

Article Materials Science, Multidisciplinary

HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations

Joshua A. Anderson et al.

COMPUTATIONAL MATERIALS SCIENCE (2020)

添加到收藏夹

Article Automation & Control Systems

Optimal feedback control of batch self-assembly processes using dynamic programming

Martha A. Grover et al.

JOURNAL OF PROCESS CONTROL (2020)

添加到收藏夹

Article Chemistry, Multidisciplinary

Exploiting Colloidal Metamaterials for Achieving Unnatural Optical Refractions

Ji-Hyeok Huh et al.

ADVANCED MATERIALS (2020)

添加到收藏夹

Review Chemistry, Physical

An Active Approach to Colloidal Self-Assembly

Stewart A. Mallory et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 69 (2018)

添加到收藏夹

Review Chemistry, Multidisciplinary

Markov State Models: From an Art to a Science

Brooke E. Husic et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

添加到收藏夹

Article Multidisciplinary Sciences

VAMPnets for deep learning of molecular kinetics

Andreas Mardt et al.

NATURE COMMUNICATIONS (2018)

添加到收藏夹

Article Multidisciplinary Sciences

Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions

Jui-Chia Chang et al.

SCIENTIFIC REPORTS (2018)

添加到收藏夹

Article Multidisciplinary Sciences

Nonequilibrium associative retrieval of multiple stored self-assembly targets

Gili Bisker et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

添加到收藏夹

Article Automation & Control Systems

A comparison of open-loop and closed-loop strategies in colloidal self-assembly

Xun Tang et al.

JOURNAL OF PROCESS CONTROL (2017)

添加到收藏夹

Review Engineering, Electrical & Electronic

A review on self-assembly in microfluidic devices

Yingying Dou et al.

JOURNAL OF MICROMECHANICS AND MICROENGINEERING (2017)

添加到收藏夹

Article Multidisciplinary Sciences

Turning statistical physics models into materials design engines

Marc Z. Miskin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

添加到收藏夹

Article Chemistry, Multidisciplinary

Optimal Feedback Controlled Assembly of Perfect Crystals

Xun Tang et al.

ACS NANO (2016)

添加到收藏夹

Article Chemistry, Multidisciplinary

Dynamic, Directed Self-Assembly of Nanoparticles via Toggled Interactions

Zachary M. Sherman et al.

ACS NANO (2016)

添加到收藏夹

Review Biophysics

Design Principles of Length Control of Cytoskeletal Structures

Lishibanya Mohapatra et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 45 (2016)

添加到收藏夹

Review Chemistry, Physical

Active colloids: Progress and challenges towards realising autonomous applications

S. J. Ebbens

CURRENT OPINION IN COLLOID & INTERFACE SCIENCE (2016)

添加到收藏夹

Article Chemistry, Physical

Communication: Inverse design for self-assembly via on-the-fly optimization

Beth A. Lindquist et al.

JOURNAL OF CHEMICAL PHYSICS (2016)

添加到收藏夹

Article Chemistry, Physical

Optimising self-assembly through time-dependent interactions

Christopher J. Fullerton et al.

JOURNAL OF CHEMICAL PHYSICS (2016)

添加到收藏夹

Review Chemistry, Multidisciplinary

Self-Assembly of Structures with Addressable Complexity

William M. Jacobs et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)

添加到收藏夹

Article Multidisciplinary Sciences

Design principles for nonequilibrium self-assembly

Michael Nguyen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

添加到收藏夹

Article Multidisciplinary Sciences

Light-induced self-assembly of active rectification devices

Joakim Stenhammar et al.

SCIENCE ADVANCES (2016)

添加到收藏夹

Review Chemistry, Physical

The Statistical Mechanics of Dynamic Pathways to Self-Assembly

Stephen Whitelam et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 66 (2015)

添加到收藏夹

Article Chemistry, Multidisciplinary

Synthetic Strategies Toward DNA-Coated Colloids that Crystallize

Yufeng Wang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

添加到收藏夹

Article Multidisciplinary Sciences

Programming colloidal phase transitions with DNA strand displacement

W. Benjamin Rogers et al.

SCIENCE (2015)

添加到收藏夹

Article Chemistry, Physical

Celebrating Soft Matter's 10th Anniversary: Approaches to program the time domain of self-assemblies

Laura Heinen et al.

SOFT MATTER (2015)

添加到收藏夹

Article Multidisciplinary Sciences

Undesired usage and the robust self-assembly of heterogeneous structures

Arvind Murugan et al.

NATURE COMMUNICATIONS (2015)

添加到收藏夹

Article Chemistry, Physical

Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model

Edina Rosta et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

添加到收藏夹

Article Chemistry, Physical

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models

Gerhard Hummer et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

添加到收藏夹

Article Multidisciplinary Sciences

Multifarious assembly mixtures: Systems allowing retrieval of diverse stored structures

Arvind Murugan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

添加到收藏夹

Article Chemistry, Physical

Using Markov state models to study self-assembly

Matthew R. Perkett et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

添加到收藏夹

Article Chemistry, Physical

Perspective: Markov models for long-timescale biomolecular dynamics

C. R. Schwantes et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

添加到收藏夹

Article Chemistry, Physical

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states

Hao Wu et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

添加到收藏夹

Article Chemistry, Physical

Nonlinear Machine Learning of Patchy Colloid Self-Assembly Pathways and Mechanisms

Andrew W. Long et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2014)

添加到收藏夹

Article Multidisciplinary Sciences

Dissipative self-assembly of particles interacting through time-oscillatory potentials

Mario Tagliazucchi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

添加到收藏夹

Article Multidisciplinary Sciences

Size limits of self-assembled colloidal structures made using specific interactions

Zorana Zeravcic et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

添加到收藏夹

Article Chemistry, Physical

Self-assembly of reconfigurable colloidal molecules

Daniel Ortiz et al.

SOFT MATTER (2014)

添加到收藏夹

Article Physics, Multidisciplinary

xTRAM: Estimating Equilibrium Expectations from Time-Correlated Simulation Data at Multiple Thermodynamic States

Antonia S. J. S. Mey et al.

PHYSICAL REVIEW X (2014)

添加到收藏夹

Article Chemistry, Multidisciplinary

Feedback Controlled Colloidal Self-Assembly

Jaime J. Juarez et al.

ADVANCED FUNCTIONAL MATERIALS (2012)

添加到收藏夹

Review Chemistry, Multidisciplinary

Predicting self-assembly: from empirism to determinism

Carlos-Andres Palma et al.

CHEMICAL SOCIETY REVIEWS (2012)

添加到收藏夹

Article Physics, Condensed Matter

Temperature as an external field for colloid-polymer mixtures: 'quenching' by heating and 'melting' by cooling

Shelley L. Taylor et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2012)

添加到收藏夹

Article Multidisciplinary Sciences

Colloids with valence and specific directional bonding

Yufeng Wang et al.

NATURE (2012)

添加到收藏夹

Article Multidisciplinary Sciences

Assembly of reconfigurable one-dimensional colloidal superlattices due to a synergy of fundamental nanoscale forces

Kaylie L. Young et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

添加到收藏夹

Article Multidisciplinary Sciences

Predictive Self-Assembly of Polyhedra into Complex Structures

Pablo F. Damasceno et al.

SCIENCE (2012)

添加到收藏夹

Article Multidisciplinary Sciences

Three-Dimensional Structures Self-Assembled from DNA Bricks

Yonggang Ke et al.

SCIENCE (2012)

添加到收藏夹

Review Biotechnology & Applied Microbiology

Colloidal systems for drug delivery: from design to therapy

Mariana Beija et al.

TRENDS IN BIOTECHNOLOGY (2012)

添加到收藏夹

Article Chemistry, Physical

Analyzing mechanisms and microscopic reversibility of self-assembly

James Grant et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

添加到收藏夹

Article Chemistry, Physical

Markov models of molecular kinetics: Generation and validation

Jan-Hendrik Prinz et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

添加到收藏夹

Article Chemistry, Multidisciplinary

DNA-Enabled Self-Assembly of Plasmonic Nanoclusters

Jonathan A. Fan et al.

NANO LETTERS (2011)

添加到收藏夹

Article Multidisciplinary Sciences

Design principles for self-assembly with short-range interactions

Sahand Hormoz et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

添加到收藏夹

Article Chemistry, Multidisciplinary

Reconfigurable Assemblies of Shape-Changing Nanorods

Trung Dac Nguyen et al.

ACS NANO (2010)

添加到收藏夹

Editorial Material Multidisciplinary Sciences

MATERIALS SCIENCE Reconfigurable colloids

Michael J. Solomon

NATURE (2010)

添加到收藏夹

Article Multidisciplinary Sciences

Lock and key colloids

S. Sacanna et al.

NATURE (2010)

添加到收藏夹

Review Biochemical Research Methods

Everything you wanted to know about Markov State Models but were afraid to ask

Vijay S. Pande et al.

METHODS (2010)

添加到收藏夹

Article Multidisciplinary Sciences

A Phenomenological Model for Predicting Melting Temperatures of DNA Sequences

Garima Khandelwal et al.

PLOS ONE (2010)

添加到收藏夹

Article Chemistry, Multidisciplinary

The Impact of Direct Nucleation Control on Crystal Size Distribution in Pharmaceutical Crystallization Processes

Mohd R. Abu Bakar et al.

CRYSTAL GROWTH & DESIGN (2009)

添加到收藏夹

Article Mathematics, Interdisciplinary Applications

DATA-BASED INFERENCE OF GENERATORS FOR MARKOV JUMP PROCESSES USING CONVEX OPTIMIZATION

Daan Crommelin et al.

MULTISCALE MODELING & SIMULATION (2009)

添加到收藏夹

Review Chemistry, Physical

Self-assembly and transformation of hybrid nano-objects and nanostructures under equilibrium and non-equilibrium conditions

Stephen Mann

NATURE MATERIALS (2009)

添加到收藏夹

Article Chemistry, Physical

Reversible self-assembly of patchy particles into monodisperse icosahedral clusters

Alex W. Wilber et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

添加到收藏夹

Article Mathematics, Applied

On choosing optimal shape parameters for RBF approximation

Gregory E. Fasshatier et al.

NUMERICAL ALGORITHMS (2007)

添加到收藏夹

Article Engineering, Chemical

Manipulation of crystal shape by cycles of growth and dissolution

Ryan C. Snyder et al.

AICHE JOURNAL (2007)

添加到收藏夹

Article Biophysics

Dynamic pathways for viral capsid assembly

Michael F. Hagan et al.

BIOPHYSICAL JOURNAL (2006)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.