134 citations · 1.1k across the 24 of their papers we have counts for
24 papers
A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals
Aleks Reinhardt, Pin Yu Chew, Bingqing Cheng
Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy…
Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers
Alexander Cumberworth, Daan Frenkel, Aleks Reinhardt
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which i…
Same and interconvertible high-pressure ice phases
Aleks Reinhardt, Mandy Bethkenhagen, Federica Coppari +3
Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our atomistic simulations show that, amongst these bcc ice phases, ices VII, VII'…
Quantum-mechanical exploration of the phase diagram of water
Aleks Reinhardt, Bingqing Cheng
The phase diagram of water harbours many mysteries: some of the phase boundaries are fuzzy, and the set of known stable phases may not be complete. Starting from liquid water and a…
Numerical calculation of free-energy barriers for entangled polymer nucleation
Xiaoliang Tang, Fucheng Tian, Tingyu Xu +2
The crystallisation of entangled polymers from their melt is investigated using computer simulation with a coarse-grained model. Using hybrid Monte Carlo simulations enables us to…
Predicting the phase diagram of titanium dioxide with random search and pattern recognition
Aleks Reinhardt, Chris J. Pickard, Bingqing Cheng
Predicting phase stabilities of crystal polymorphs is central to computational materials science and chemistry. Such predictions are challenging because they first require searchin…
Phase behaviour of empirical potentials of titanium dioxide
Aleks Reinhardt
In recent years, several relatively similar empirical models of titanium dioxide have been proposed as reparameterisations of the potential of Matsui and Akaogi, with the Buckingha…
Microscopic analysis of thermo-orientation in systems of off-centre Lennard-Jones particles
Robert L. Jack, Peter Wirnsberger, Aleks Reinhardt
When fluids of anisotropic molecules are placed in temperature gradients, the molecules may align themselves along the gradient: this is called thermo-orientation. We discuss the t…
Lattice models and Monte Carlo methods for simulating DNA origami self-assembly
Alexander Cumberworth, Aleks Reinhardt, Daan Frenkel
The optimal design of DNA origami systems that assemble rapidly and robustly is hampered by the lack of a model for self-assembly that is sufficiently detailed yet computationally…
Theoretical prediction of thermal polarisation
Peter Wirnsberger, Christoph Dellago, Daan Frenkel +1
We present a mean-field theory to explain the thermo-orientation effect in an off-centre Stockmayer fluid. This effect is the underlying cause of thermally induced polarisation and…
Direct observation and rational design of nucleation behavior in addressable self-assembly
Martin Sajfutdinow, William M. Jacobs, Aleks Reinhardt +2
In order to optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model s…
Investigating the role of boundary bricks in DNA brick self-assembly
Hannah Wayment-Steele, Daan Frenkel, Aleks Reinhardt
In the standard DNA brick set-up, distinct 32-nucleotide strands of single-stranded DNA are each designed to bind specifically to four other such molecules. Experimentally, it has…
Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal
Aleks Reinhardt, John S. Schreck, Flavio Romano +1
We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable…
DNA brick self-assembly with an off-lattice potential
Aleks Reinhardt, Daan Frenkel
We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy…
Effects of co-ordination number on the nucleation behaviour in many-component self-assembly
Aleks Reinhardt, Chon Pan Ho, Daan Frenkel
We report canonical and grand-canonical lattice Monte Carlo simulations of the self-assembly of addressable structures comprising hundreds of distinct component types. The nucleati…
Rational design of self-assembly pathways for complex multicomponent structures
William M. Jacobs, Aleks Reinhardt, Daan Frenkel
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits o…
Theoretical prediction of free-energy landscapes for complex self-assembly
William M. Jacobs, Aleks Reinhardt, Daan Frenkel
We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key fact…
Effects of surface interactions on heterogeneous ice nucleation for a monatomic water model
Aleks Reinhardt, Jonathan P. K. Doye
Despite its importance in atmospheric science, much remains unknown about the microscopic mechanism of heterogeneous ice nucleation. In this work, we perform hybrid Monte Carlo sim…
Numerical evidence for nucleated self-assembly of DNA brick structures
Aleks Reinhardt, Daan Frenkel
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great…
Homogeneous TIP4P/2005 ice nucleation at low supercooling
Aleks Reinhardt, Jonathan P. K. Doye
We present a partial free energy profile for the homogeneous nucleation of ice using an all-atom model of water at low supercooling, at which ice growth dynamics are reasonably acc…
Computing phase diagrams for a quasicrystal-forming patchy-particle system
Aleks Reinhardt, Flavio Romano, Jonathan P. K. Doye
We introduce an approach to computing the free energy of quasicrystals, which we use to calculate phase diagrams for systems of two-dimensional patchy particles with five regularly…
Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water
Aleks Reinhardt, Jonathan P. K. Doye, Eva G. Noya +1
We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of…
Free energy landscapes for homogeneous nucleation of ice for a monatomic water model
Aleks Reinhardt, Jonathan P. K. Doye
We simulate the homogeneous nucleation of ice from supercooled liquid water at 220 K in the isobaric-isothermal ensemble using the MW monatomic water potential. Monte Carlo simulat…
Reentrant phase behaviour for systems with competition between phase separation and self-assembly
Aleks Reinhardt, Alexander J. Williamson, Jonathan P. K. Doye +3
In patchy particle systems where there is competition between the self-assembly of finite clusters and liquid-vapour phase separation, reentrant phase behaviour is observed, with t…