Multiscale simulations for understanding the evolution and mechanism of hierarchical peptide self-assembly

Concentration Dependent Self-Assembly of TrK-NGF Receptor Derived Tripeptide: New Insights from Experiment and Computer Simulations

(2017) Parikshit Moitra et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

(2017) Rachael A. Mansbach et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Biological Photothermal Nanodots Based on Self-Assembly of Peptide–Porphyrin Conjugates for Antitumor Therapy

(2017) Qianli Zou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Intramolecular cation–π interactions in protonated phenylalanine derivatives

(2017) Weiqiang Fu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Injectable Self-Assembled Dipeptide-Based Nanocarriers for Tumor Delivery and Effective In Vivo Photodynamic Therapy

(2016) Kai Ma et al.   ACS Applied Materials & Interfaces

Trace Solvent as a Predominant Factor To Tune Dipeptide Self-Assembly

(2016) Juan Wang et al.   ACS Nano

Expanding the Nanoarchitectural Diversity Through Aromatic Di- and Tri-Peptide Coassembly: Nanostructures and Molecular Mechanisms

(2016) Cong Guo et al.   ACS Nano

Mimicking Primitive Photobacteria: Sustainable Hydrogen Evolution Based on Peptide-Porphyrin Co-Assemblies with a Self-Mineralized Reaction Center

(2016) Kai Liu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Simple Peptide-Tuned Self-Assembly of Photosensitizers towards Anticancer Photodynamic Therapy

(2016) Kai Liu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Peptide self-assembly: thermodynamics and kinetics

(2016) Juan Wang et al.   CHEMICAL SOCIETY REVIEWS

Hierarchical processes inβ-sheet peptide self-assembly from the microscopic to the mesoscopic level

(2016) Li Deng et al.   Chinese Physics B

Tuning self-assembled morphology of the Aβ(16–22) peptide by substitution of phenylalanine residues

(2016) Jiqian Wang et al.   COLLOIDS AND SURFACES B-BIOINTERFACES

Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures

(2016) Glauco G. Almeida et al.   Journal of Chemical Theory and Computation

Different nanostructures caused by competition of intra- and inter- β -sheet interactions in hierarchical self-assembly of short peptides

(2016) Peng Zhou et al.   JOURNAL OF COLLOID AND INTERFACE SCIENCE

Sodium chloride's effect on self-assembly of diphenylalanine bilayer

(2016) Junpyo Kwon et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assembly of Triblock Amphiphilic Peptides into One-Dimensional Aggregates and Network Formation

(2016) Beytullah Ozgur et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies

(2016) Qiang Cui et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Organization and Structure of Branched Amphipathic Oligopeptide Bilayers

(2016) Zhiguang Jia et al.   LANGMUIR

In situ real-time imaging of self-sorted supramolecular nanofibres

(2016) Shoji Onogi et al.   Nature Chemistry

Energy landscapes and functions of supramolecular systems

(2016) Faifan Tantakitti et al.   NATURE MATERIALS

Fmoc–RGDS based fibrils: atomistic details of their hierarchical assembly

(2016) David Zanuy et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Dipeptide concave nanospheres based on interfacially controlled self-assembly: from crescent to solid

(2016) Juan Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

CHARMM force field parameterization protocol for self-assembling peptide amphiphiles: the Fmoc moiety

(2016) I. Ramos Sasselli et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

On the origin of the great rigidity of self-assembled diphenylalanine nanotubes

(2016) Pavel Zelenovskiy et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Molecular and mesoscale mechanism for hierarchical self-assembly of dipeptide and porphyrin light-harvesting system

(2016) Kai Liu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Using experimental and computational energy equilibration to understand hierarchical self-assembly of Fmoc-dipeptide amphiphiles

(2016) I. R. Sasselli et al.   Soft Matter

Water-driven stabilization of diphenylalanine nanotube structures

(2016) T. Andrade-Filho et al.   THEORETICAL CHEMISTRY ACCOUNTS

Water ordering controls the dynamic equilibrium of micelle–fibre formation in self-assembly of peptide amphiphiles

(2016) Sanket A. Deshmukh et al.   Nature Communications

The self-assembly mechanism of tetra-peptides from the motif of β-amyloid peptides: a combined coarse-grained and all-atom molecular dynamics simulation

(2016) Lijun Liang et al.   RSC Advances

Peptide-Modulated Self-Assembly of Chromophores toward Biomimetic Light-Harvesting Nanoarchitectonics

(2015) Qianli Zou et al.   ADVANCED MATERIALS

Functional architectures based on self-assembly of bio-inspired dipeptides: Structure modulation and its photoelectronic applications

(2015) Chengjun Chen et al.   ADVANCES IN COLLOID AND INTERFACE SCIENCE

Diphenylalanine Self Assembly: Novel Ion Mobility Methods Showing the Essential Role of Water

(2015) Thanh D. Do et al.   ANALYTICAL CHEMISTRY

Self-assembled peptide nanotubes as electronic materials: An evaluation from first-principles calculations

(2015) Brahim Akdim et al.   APPLIED PHYSICS LETTERS

Sequence-Dependent Structural Stability of Self-Assembled Cylindrical Nanofibers by Peptide Amphiphiles

(2015) Iris W. Fu et al.   BIOMACROMOLECULES

Supramolecular Polymers: Historical Development, Preparation, Characterization, and Functions

(2015) Liulin Yang et al.   CHEMICAL REVIEWS

Computational Approaches to Understanding the Self-assembly of Peptide-based Nanostructures

(2015) Tell Tuttle   ISRAEL JOURNAL OF CHEMISTRY

Mesoscopic Simulation of Phospholipid Membranes, Peptides, and Proteins with Molecular Fragment Dynamics

(2015) Andreas Truszkowski et al.   Journal of Chemical Information and Modeling

SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics

(2015) Leonardo Darré et al.   Journal of Chemical Theory and Computation

Martini Coarse-Grained Force Field: Extension to DNA

(2015) Jaakko J. Uusitalo et al.   Journal of Chemical Theory and Computation

Controlling and imaging biomimetic self-assembly

(2015) Alessandro Aliprandi et al.   Nature Chemistry

Supramolecular systems chemistry

(2015) Elio Mattia et al.   Nature Nanotechnology

Regulation and aggregation of intrinsically disordered peptides

(2015) Zachary A. Levine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Self-assembly of dipeptide sodium salts derived from alanine: a molecular dynamics study

(2015) Jichao Sun et al.   RSC Advances

Multifunctional Porous Microspheres Based on Peptide-Porphyrin Hierarchical Co-Assembly

(2014) Qianli Zou et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Tail of Two Peptide Amphiphiles: Effect of Conjugation with Hydrophobic Polymer on Folding of Peptide Sequences

(2014) Brian K. Chu et al.   BIOMACROMOLECULES

Molecular Assembly of Schiff Base Interactions: Construction and Application

(2014) Yi Jia et al.   CHEMICAL REVIEWS

Design of nanostructures based on aromatic peptide amphiphiles

(2014) Scott Fleming et al.   CHEMICAL SOCIETY REVIEWS

A Coarse-Grained Model for Peptide Aggregation on a Membrane Surface

(2014) Alex Morriss-Andrews et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics Study of Surfactant-Like Peptide Based Nanostructures

(2014) Guilherme Colherinhas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Raman Optical Activity of a Cyclic Dipeptide Analyzed by Quantum Chemical Calculations Combined with Molecular Dynamics Simulations

(2014) Hiroyasu Urago et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Origin of the Self-Assembled Morphological Difference Caused by Varying the Order of Charged Residues in Short Peptides

(2014) Li Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theoretical Insight into the Relationship between the Structures of Antimicrobial Peptides and Their Actions on Bacterial Membranes

(2014) Licui Chen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles

(2014) Yoann Cote et al.   Journal of Physical Chemistry C

β Sheets Not Required: Combined Experimental and Computational Studies of Self-Assembly and Gelation of the Ester-Containing Analogue of an Fmoc-Dipeptide Hydrogelator

(2014) Kevin M. Eckes et al.   LANGMUIR

Solvent Effects on Kinetic Mechanisms of Self-Assembly by Peptide Amphiphiles via Molecular Dynamics Simulations

(2014) Iris W. Fu et al.   LANGMUIR

Role of Hydrophobicity on Self-Assembly by Peptide Amphiphiles via Molecular Dynamics Simulations

(2014) Iris W. Fu et al.   LANGMUIR

Recent Advances in Nanoscale Bioinspired Materials

(2014) Melik C. Demirel et al.   MACROMOLECULAR BIOSCIENCE

Triphenylalanine peptides self-assemble into nanospheres and nanorods that are different from the nanovesicles and nanotubes formed by diphenylalanine peptides

(2014) Cong Guo et al.   Nanoscale

Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels

(2014) Pim W. J. M. Frederix et al.   Nature Chemistry

Martini Force Field Parameters for Glycolipids

(2013) César A. López et al.   Journal of Chemical Theory and Computation

Characteristic Raman Optical Activity Signatures of Protein β-Sheets

(2013) Thomas Weymuth et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effects of pH and Charge State on Peptide Assembly: The YVIFL Model System

(2013) Thanh D. Do et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of Solvent on the Self-Assembly of Dialanine and Diphenylalanine Peptides

(2013) Anastassia N. Rissanou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Infrared, Vibrational Circular Dichroism, and Raman Spectral Simulations for β-Sheet Structures with Various Isotopic Labels, Interstrand, and Stacking Arrangements Using Density Functional Theory

(2013) William R. W. Welch et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Insights into Diphenylalanine Nanotube Assembly: All-Atom Simulations of Oligomerization

(2013) Joohyun Jeon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ferrocenoyl Phenylalanine: A New Strategy Toward Supramolecular Hydrogels with Multistimuli Responsive Properties

(2013) Zhifang Sun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Higher Order Amyloid Fibril Structure by MAS NMR and DNP Spectroscopy

(2013) Galia T. Debelouchina et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Why Are Diphenylalanine-Based Peptide Nanostructures so Rigid? Insights from First Principles Calculations

(2013) Ido Azuri et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Assessing the Utility of Infrared Spectroscopy as a Structural Diagnostic Tool for β-Sheets in Self-Assembling Aromatic Peptide Amphiphiles

(2013) Scott Fleming et al.   LANGMUIR

Solvent-Induced Handedness Inversion of Dipeptide Sodium Salts Derived from Alanine

(2013) Yi Li et al.   LANGMUIR

Terminal Is Important for the Helicity of the Self-Assemblies of Dipeptides Derived from Alanine

(2013) Yitai Fu et al.   LANGMUIR

Dissecting the structural determinants for the difference in mechanical stability of silk and amyloid beta-sheet stacks

(2013) Senbo Xiao et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Molecular insights into aggregates made of amphiphilic Fmoc-tetrapeptides

(2013) Daniel E. López-Pérez et al.   Soft Matter

The Role of Electrostatics and Temperature on Morphological Transitions of Hydrogel Nanostructures Self-Assembled by Peptide Amphiphiles Via Molecular Dynamics Simulations

(2013) Iris W. Fu et al.   Advanced Healthcare Materials

Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes

(2012) Cong Guo et al.   ACS Nano

A molecular dynamics simulation of N-(fluorenyl-9-methoxycarbonyl)-dipeptides supramolecular hydrogel

(2012) Heng Zhang et al.   COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS

β-sheet propensity controls the kinetic pathways and morphologies of seeded peptide aggregation

(2012) Alex Morriss-Andrews et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetic pathways to peptide aggregation on surfaces: The effects of β-sheet propensity and surface attraction

(2012) Alex Morriss-Andrews et al.   JOURNAL OF CHEMICAL PHYSICS

Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion

(2012) Han Wang et al.   Journal of Chemical Theory and Computation

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

(2012) Elio A. Cino et al.   Journal of Chemical Theory and Computation

Polarizable Molecular Dynamics Simulations of Aqueous Dipeptides

(2012) Tugba G. Kucukkal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly

(2012) Scott P. Carmichael et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water-Sensitive High-Frequency Molecular Vibrations in Self-Assembled Diphenylalanine Nanotubes

(2012) Xinglong Wu et al.   Journal of Physical Chemistry C

DPD Simulation of Protein Conformations: From α-Helices to β-Structures

(2012) Aleksey Vishnyakov et al.   Journal of Physical Chemistry Letters

Modeling the Self-Assembly of Peptide Amphiphiles into Fibers Using Coarse-Grained Molecular Dynamics

(2012) One-Sun Lee et al.   NANO LETTERS

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Determination of Absolute Configuration of Chiral Molecules Using Vibrational Optical Activity: A Review

(2011) Yanan He et al.   APPLIED SPECTROSCOPY

Spontaneous Formation of Twisted Aβ16-22 Fibrils in Large-Scale Molecular-Dynamics Simulations

(2011) Mookyung Cheon et al.   BIOPHYSICAL JOURNAL

Self-assembly of polypeptide-based copolymers into diverse aggregates

(2011) Chunhua Cai et al.   CHEMICAL COMMUNICATIONS

Effects of surface interactions on peptide aggregate morphology

(2011) Alex Morriss-Andrews et al.   JOURNAL OF CHEMICAL PHYSICS

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly

(2011) Pim W. J. M. Frederix et al.   Journal of Physical Chemistry Letters

Calculation of Raman Optical Activity Spectra of Methyl-β-d-Glucose Incorporating a Full Molecular Dynamics Simulation of Hydration Effects

(2011) James R. Cheeseman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers

(2011) One-Sun Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models

(2011) Ozge Engin et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Multi-hierarchical self-assembly of a collagen mimetic peptide from triple helix to nanofibre and hydrogel

(2011) Lesley E. R. O'Leary et al.   Nature Chemistry

The amyloid cascade hypothesis for Alzheimer's disease: an appraisal for the development of therapeutics

(2011) Eric Karran et al.   NATURE REVIEWS DRUG DISCOVERY

Multiscale modeling of soft matter: scaling of dynamics

(2011) Dominik Fritz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif

(2011) V. Castelletto et al.   Soft Matter

Self-assembly of peptide amphiphiles: From molecules to nanostructures to biomaterials

(2010) Honggang Cui et al.   BIOPOLYMERS

Self-assembly and application of diphenylalanine-based nanostructures

(2010) Xuehai Yan et al.   CHEMICAL SOCIETY REVIEWS

PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification

(2010) Wei Han et al.   Journal of Chemical Theory and Computation

PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides

(2010) Wei Han et al.   Journal of Chemical Theory and Computation

Studies on the Structure and Stability of Cyclic Peptide Based Nanotubes Using Oligomeric Approach: A Computational Chemistry Investigation

(2010) R. Vijayaraj et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Elementary Building Blocks of Self-Assembled Peptide Nanotubes

(2010) Nadav Amdursky et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Extending the PRIME model for protein aggregation to all 20 amino acids

(2010) Mookyung Cheon et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Multiscale Modeling of Proteins

(2009) Valentina Tozzini   ACCOUNTS OF CHEMICAL RESEARCH

Role of Water in Directing Diphenylalanine Assembly into Nanotubes and Nanowires

(2009) Jangbae Kim et al.   ADVANCED MATERIALS

Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations

(2009) Phanourios Tamamis et al.   BIOPHYSICAL JOURNAL

Challenges and Perspectives in Biomolecular Simulations: From the Atomistic Picture to Multiscale Modeling

(2009) Michele Cascella et al.   CHIMIA

Assembly dynamics of two-β sheets revealed by molecular dynamics simulations

(2009) Weixin Xu et al.   JOURNAL OF CHEMICAL PHYSICS

Effect of β-sheet propensity on peptide aggregation

(2009) Giovanni Bellesia et al.   JOURNAL OF CHEMICAL PHYSICS

Diversity of kinetic pathways in amyloid fibril formation

(2009) Giovanni Bellesia et al.   JOURNAL OF CHEMICAL PHYSICS

Martini Coarse-Grained Force Field: Extension to Carbohydrates

(2009) Cesar A. López et al.   Journal of Chemical Theory and Computation

Protected Peptide Nanoparticles: Experiments and Brownian Dynamics Simulations of the Energetics of Assembly

(2009) Ting Chen et al.   NANO LETTERS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Role of Water in Mediating the Assembly of Alzheimer Amyloid-β Aβ16−22 Protofilaments

(2008) Mary Griffin Krone et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent

(2008) Yan Lu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS