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1. Experimental observations of fractal landscape dynamics in a dense emulsion

   https://doi.org/10.1039/D3SM00852E  

   Rodríguez-Cruz, Clary; Molaei, Mehdi; Thirumalaiswamy, Amruthesh; Feitosa, Klebert; Manoharan, Vinothan N; Sivarajan, Shankar; Reich, Daniel H; Riggleman, Robert A; Crocker, John C (September 2023, Soft Matter)

   Many soft and biological materials display so-called ‘soft glassy’ dynamics; their constituents undergo anomalous random motions and complex cooperative rearrangements. A recent simulation model of one soft glassy material, a coarsening foam, suggested that the random motions of its bubbles are due to the system configuration moving over a fractal energy landscape in high-dimensional space. Here we show that the salient geometrical features of such high-dimensional fractal landscapes can be explored and reliably quantified, using empirical trajectory data from many degrees of freedom, in a model-free manner. For a mayonnaise-like dense emulsion, analysis of the observed trajectories of oil droplets quantitatively reproduces the high-dimensional fractal geometry of the configuration path and its associated local energy minima generated using a computational model. That geometry in turn drives the droplets’ complex random motion observed in real space. Our results indicate that experimental studies can elucidate whether the similar dynamics in different soft and biological materials may also be due to fractal landscape dynamics. 

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2. Two-step crystallization and solid–solid transitions in binary colloidal mixtures

   https://doi.org/10.1073/pnas.2008561117  

   Fang, Huang; Hagan, Michael F.; Rogers, W. Benjamin (November 2020, Proceedings of the National Academy of Sciences)

   null (Ed.)

   Crystallization is fundamental to materials science and is central to a variety of applications, ranging from the fabrication of silicon wafers for microelectronics to the determination of protein structures. The basic picture is that a crystal nucleates from a homogeneous fluid by a spontaneous fluctuation that kicks the system over a single free-energy barrier. However, it is becoming apparent that nucleation is often more complicated than this simple picture and, instead, can proceed via multiple transformations of metastable structures along the pathway to the thermodynamic minimum. In this article, we observe, characterize, and model crystallization pathways using DNA-coated colloids. We use optical microscopy to investigate the crystallization of a binary colloidal mixture with single-particle resolution. We observe classical one-step pathways and nonclassical two-step pathways that proceed via a solid–solid transformation of a crystal intermediate. We also use enhanced sampling to compute the free-energy landscapes corresponding to our experiments and show that both one- and two-step pathways are driven by thermodynamics alone. Specifically, the two-step solid–solid transition is governed by a competition between two different crystal phases with free energies that depend on the crystal size. These results extend our understanding of available pathways to crystallization, by showing that size-dependent thermodynamic forces can produce pathways with multiple crystal phases that interconvert without free-energy barriers and could provide approaches to controlling the self-assembly of materials made from colloids. 

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3. Consensus-based adaptive sampling and approximation for high-dimensional energy landscapes

   Lyu, Liyao; Lei, Huan (May 2025, arXivorg)

   We present a consensus-based framework that unifies phase space exploration with posterior-residual-based adaptive sampling for surrogate construction in high-dimensional energy landscapes. Unlike standard approximation tasks where sampling points can be freely queried, systems with complex energy landscapes such as molecular dynamics (MD) do not have direct access to arbitrary sampling regions due to the physical constraints and energy barriers; the surrogate construction further relies on the dynamical exploration of phase space, posing a significant numerical challenge. We formulate the problem as a minimax optimization that jointly adapts both the surrogate approximation and residual-enhanced sampling. The construction of free energy surfaces (FESs) for high-dimensional collective variables (CVs) of MD systems is used as a motivating example to illustrate the essential idea. Specifically, the maximization step establishes a stochastic interacting particle system to impose adaptive sampling through both exploitation of a Laplace approximation of the max-residual region and exploration of uncharted phase space via temperature control. The minimization step updates the FES surrogate with the new sample set. Numerical results demonstrate the effectiveness of the present approach for biomolecular systems with up to 30 CVs. While we focus on the FES construction, the developed framework is general for efficient surrogate construction for complex systems with high-dimensional energy landscapes. 

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4. Modeling the energetic tail of a dusty plasma's electron energy distribution and its effect on dust grain charge and behavior

   https://doi.org/10.1063/5.0145209  

   Nicolov, André; Bellan, Paul M (August 2023, Physics of Plasmas)

   A model for a weakly ionized dusty plasma is proposed in which UV or x-ray radiation continuously creates free electrons at high energy, which then cool through collisions with a cold neutral gas before recombining. The transition of a free electron from high energy at birth to low energy at demise implies that the electron energy distribution is not the simple Maxwellian of an isolated system in thermal equilibrium, but instead has a high-energy tail that depends on the recombination time. This tail can have a major effect on dust grain charging because the flux of tail electrons can be substantial even if the density of tail electrons is small. Detailed analytic and numerical calculations of dust grain charging show that situations exist in which a small high-energy tail dominates charge behavior. This implies that dust grain charge in terrestrial and space dusty plasmas may be significantly underestimated if a Maxwellian distribution is assumed and the non-thermal dynamics are neglected. 

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5. REVO: Resampling of ensembles by variation optimization

   https://doi.org/10.1063/1.5100521  

   Donyapour, Nazanin; Roussey, Nicole_M; Dickson, Alex (June 2019, The Journal of Chemical Physics)

   Conventional molecular dynamics simulations are incapable of sampling many important interactions in biomolecular systems due to their high dimensionality and rough energy landscapes. To observe rare events and calculate transition rates in these systems, enhanced sampling is a necessity. In particular, the study of ligand-protein interactions necessitates a diverse ensemble of protein conformations and transition states, and for many systems, this occurs on prohibitively long time scales. Previous strategies such as WExplore that can be used to determine these types of ensembles are hindered by problems related to the regioning of conformational space. Here, we propose a novel, regionless, enhanced sampling method that is based on the weighted ensemble framework. In this method, a value referred to as “trajectory variation” is optimized after each cycle through cloning and merging operations. This method allows for a more consistent measurement of observables and broader sampling resulting in the efficient exploration of previously unexplored conformations. We demonstrate the performance of this algorithm with the N-dimensional random walk and the unbinding of the trypsin-benzamidine system. The system is analyzed using conformation space networks, the residence time of benzamidine is confirmed, and a new unbinding pathway for the trypsin-benzamidine system is found. We expect that resampling of ensembles by variation optimization will be a useful general tool to broadly explore free energy landscapes. 

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