28 papers · ranked by Valyu relevance
Mehdi Bouzid, Jader Colombo, Lucas Vieira Barbosa, Emanuela Del Gado
Soft solids with tunable mechanical response are at the core of new material technologies, but a crucial limit for applications is their progressive aging over time, which dramatically affects their functionalities. The generally accepted paradigm is that such aging is gradual and its origin is in slower than…
Michael P.N. Juniper, Arthur V. Straube, Rut Besseling, Dirk G.A.L. Aarts + 1 more
'Dirk G.A.L. Aarts' 'Roel P.A. Dullens'] Synchronization of coupled oscillators has been scrutinized for over three centuries, from Huygens' pendulum clocks to physiological rhythms. One such synchronization phenomenon, dynamic mode locking, occurs when naturally oscillating processes are driven by an externally…
Hua Tong, Hajime Tanaka
Glass transition is characterised by drastic dynamical slowing down upon cooling, accompanied by growing spatial heterogeneity. Its rationalisation by subtle changes in the liquid structure has been long debated but remains elusive, due to intrinsic difficulty in detecting the underlying complex structural ordering.…
Elizabeth D. White, Younan Li, Rachel Kadzik, Yuqing Qiu + 2 more
Cell polarization, migration, and cytokinesis rely on flows of the cell cortex, a network of actin filaments, cross-linkers, and motors beneath the plasma membrane of animal cells. While actin network architecture, assembly dynamics, and motor activity are known to be important for cortical flows, how their modulation…
Bezia Lemma, Linnea M. Lemma, Stephanie C. Ems-McClung, Claire E. Walczak + 2 more
'Claire E. Walczak' 'Zvonimir Dogic' 'Daniel J. Needleman'] Connecting the large-scale emergent behaviors of active cytoskeletal materials to the microscopic properties of their constituents is a challenge due to a lack of data on the multiscale dynamics and structure of such systems. We approach this problem by…
Authors not listed
The formation and modulation of biomolecular condensates as well as their structural and dynamic properties are determined by an intricate interplay of different driving forces, which down at the microscopic scale involve molecular interactions of the biological macromolecules and the surrounding solvent and ions.…
Authors not listed
Soft matter is characterized by its relatively strong response to external and internal influences. A soft piece of rubber or biological tissue can be easily deformed between our fingers using muscle force, whereas a steel rod does not show visible deformations detectable by eye. We use theoretical calculations and…
M. Kurzynski, P. Chelminiak
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics of conformational transitions which often manifests in fluctuating rates of the catalyzed processes…
Jan Gieseler, James Millen
Levitated Nanoparticles have received much attention for their potential to perform quantum mechanical experiments even at room temperature. However, even in the regime where the particle dynamics are purely classical, there is a lot of interesting physics that can be explored. Here we review the application of…
Karthika Krishna Kumar, Juliana Caspers, Félix Ginot, Matthias Krüger + 1 more
'Matthias Krüger' 'Clemens Bechinger'] When a colloidal probe is forced through a viscoelastic fluid which is characterized by a long stress-relaxation time, the fluid is excited out of equilibrium. This is leading to a number of interesting effects including a non-trivial recoil of the probe when the driving force is…
A L Nord, A F Pols, M Depken, F Pedaci
Molecular motors convert chemical or electrical energy into mechanical displacement, either linear or rotary. Under ideal circumstances, single-molecule measurements can spatially and temporally resolve individual steps of the motor, revealing important properties of the underlying mechanochemical process.…
Amine Ammar, Francisco Chinesta, Rudy Valette
Characterizing complex material consists in establishing the relationship between flow rheology during forming processes and the induced micro-structural state that affects directly the final mechanical properties of the formed parts. It is necessary that research activities reach to address the coupling between…
Simon Bienewald, Diego M. Fieguth, James R. Anglin, Roberto Zivieri + 1 more
Thought experiments like Maxwell’s Demon or the Smoluchowski-Feynman Ratchet can help in pursuing the microscopic origin of the Second Law of Thermodynamics. Here we present a more sophisticated mechanical system than a ratchet, consisting of a Hamiltonian (non-Brownian) active particle which can harvest energy from an…
Nicholas M. Boffi, Yipei Guo, Chris H. Rycroft, Ariel Amir
The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of…
Benjamin S. Hanson, Daniel J. Read
Many biophysical systems and proteins undergo mesoscopic conformational changes in order to perform their biological function. However, these conformational changes often result from a cascade of atomistic interactions within a much larger overall object. For simulations of such systems, the computational cost of…
Stuart J. Box, Michael P. Allen, David B. Phillips, Stephen H. Simpson
'Stephen H. Simpson'] We consider the basic, thermodynamic properties of an elementary micro-machine operating at colloidal length scales. In particular, we track and analyse the driven stochastic motion of a carefully designed micro-propeller rotating unevenly in an optical tweezers, in water. In this intermediate…
Martina Crippa, Claudio Perego, Anna de Marco, Giovanni M. Pavan
Supramolecular polymers are composed of monomers that self-assemble non-covalently, generating distributions of monodimensional fibres in continuous communication with each other and with the surrounding solution. Fibres, exchanging molecular species, and external environment constitute a sole complex system, which…
Ignacio A. Martínez, Édgar Roldán, Luis Dinís, Dmitri Petrov + 1 more
'Raúl A. Rica'] We experimentally realize quasistatic adiabatic processes using a single optically-trapped microsphere immersed in water whose effective temperature is controlled by an external random electric field. A full energetic characterization of adiabatic processes that preserve either the position distribution…
Authors not listed
Atomistic simulations provide essential mechanistic insights into chemical processes, yet many important phenomena in chemistry and materials science occur on timescales that are inaccessible to molecular dynamics. Existing computational approaches force a choice between atomic resolution on relatively short timescales…
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Molecular dynamics (MD) and hybrid quantum–classical (QM/MM) methods provide powerful tools for simulating chemical and biological systems, yet their application to long-timescale, strongly coupled processes remains limited by non-integrability, chaotic sensitivity, and extreme time-scale separation. These limitations…
Jonathan Bunyan, Alexander F. Vakakis, Sameh Tawfick
We study impulse response in 1-D homogeneous micro-granular chains on a linear elastic substrate. Micro-granular interactions are analytically described by the Schwarz contact model which includes nonlinear compressive as well as snap-to/from-contact adhesive effects forming a hysteretic loop in the force deformation…
Jun Li, Ziluo Zhang, Zhanglin Hou, Kento Yasuda + 2 more
'Shigeyuki Komura'] We discuss and compare the statistical properties of two stochastic three-sphere micromachines, i.e., odd micromachine and thermal micromachine. We calculate the steady state time-correlation functions for these micromachines and decompose them into the symmetric and antisymmetric parts. In both…
Isamu Sou, Yuto Hosaka, Kento Yasuda, Shigeyuki Komura
We discuss the non-equilibrium statistical mechanics of a thermally driven micromachine consisting of three spheres and two harmonic springs [Y. Hosaka et al., J. Phys. Soc. Jpn. 86, 113801 (2017)]. We obtain the non-equilibrium steady state probability distribution function of such a micromachine and calculate its…
Ricky Nencini, Morgan Regnier, Sofia Backlund, Efstathia Mantzari + 2 more
Dynamic interactions between peptides and lipid membranes are crucial in many biological processes and biomedical applications However, monitoring of peptide dynamics in a membrane environment has been limited by the lack of experimental methods that could directly detect the fast (picosecond to nanosecond) timescale…
Lei Song, Dingyi Pan, Nhan Phan-Thien
Inertia effects in the Langevin dynamics of a lopsided elastic dumbbell are investigated using exponential-time-differencing (ETD) integrators for the corresponding stiff stochastic equations at small mass limit. Starting from the bead-level underdamped Langevin model, we formulate the dynamics in modal coordinates…
Authors not listed
The rapid progress in Artificial Intelligence (AI) has led to extraordinary achievements across various domains, significantly impacting every aspect of daily life. This advancement is also revolutionizing research in numerous scientific areas, particularly within bioinformatics, chemistry, pharmaceuticals, and…
Isamu Sou, Yuto Hosaka, Kento Yasuda, Shigeyuki Komura
We discuss the non-equilibrium properties of a thermally driven micromachine consisting of three spheres which are in equilibrium with independent heat baths characterized by different temperatures. Within the framework of a linear stochastic Langevin description, we calculate the timedependent average irreversibility…
Jane Kondev, Marc Kirschner, Hernan G. Garcia, Gabriel L. Salmon + 1 more
Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose, structure or function is achieved. A classic example is the way in which…