Role of Entropy in Colloidal Self-Assembly

Rocha, Brunno C.; Paul, Sanjib; Vashisth, Harish

doi:10.3390/e22080877

Cited by 25 publications

(22 citation statements)

References 110 publications

(127 reference statements)

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“…Similar, though more limited, ribosome associations were previously observed in attack phase, particularly in a B. bacteriovorus mutant with an even more tightly condensed nucleoid than wild-type cells (Borgnia et al, 2008; Butan et al, 2011), and in some attack-phase cells in this study. One possibility for this ribosome lattice is that it is a depletion effect resulting from entropic forces encouraging large objects to aggregate on a surface (Asakura and Oosawa, 1954, 1958; Rocha et al, 2020). However, we did not observe the effect on other cell surfaces such as the inner membrane, nor in other stages of the cell cycle, so we think this unlikely.…”

Section: Discussionmentioning

confidence: 99%

Dynamic structural adaptations enable the endobiotic predation ofbdellovibrio bacteriovorus

Kaplan

Chang

Oikonomou

et al. 2022

Preprint

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Bdellovibrio bacteriovorusis an endobiotic microbial predator that offers promise as a living antibiotic for its ability to kill Gram-negative bacteria, including human pathogens. Even after six decades of study, fundamental details of its predation cycle remain mysterious. Here, we used cryo-electron tomography to comprehensively image the lifecycle ofB. bacteriovorusat nanometer-scale resolution. In addition to providing the first high-resolution images of predation in a native (hydrated, unstained) state, we also discover several surprising features of the process, including novel macromolecular complexes involved in prey attachment/invasion and a flexible portal structure lining a hole in the prey peptidoglycan that tightly seals the prey outer membrane around the predator during entry. Unexpectedly, we find thatB. bacteriovorusdoes not shed its flagellum during invasion, but rather resorbs it into its periplasm for degradation. Finally, following replication and division in the bdelloplast, we observe a transient and extensive ribosomal lattice on the condensedB. bacteriovorusnucleoid.Graphical abstract

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Section: Discussionmentioning

confidence: 99%

Dynamic structural adaptations enable the endobiotic predation ofbdellovibrio bacteriovorus

Kaplan

Chang

Oikonomou

et al. 2022

Preprint

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“…In what follows, a select few of the applications of fluctuation theorems are summarized and discussed. Micro-sized and nano-sized machines that are primarily entropy-driven can be realized in principle for a myriad of medical and industrial applications [43], [44]. More recently, significant advances made in the area of stochastic thermodynamics have shown that in far-from-equilibrium classical systems, random fluctuations are naturally constrained by the rate of entropy production through certain thermodynamic uncertainty relations [45]- [48].…”

Section: Discussionmentioning

confidence: 99%

A Theoretical Analysis of the Transient Fluctuation Theorem for Accelerated Colloidal Systems in the Long-Time Limit

Lokare¹

2022

Preprint

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A quantitative description of the second law of thermodynamics in small scale systems and over short time scales comes from various fluctuation theorems. The applicability of the transient fluctuation theorem in particular to small scale systems perturbed from an initial equilibrium steady-state distribution has been demonstrated both theoretically and experimentally in several works over the past few decades. In addition, some experimental works in the past have also made successful attempts to demonstrate the applicability of the fluctuation theorem to small scale systems evolving from a certain nonequilibrium steady-state distribution over relatively long time scales. To this end, this paper seeks to demonstrate the transient fluctuation theorem for a Brownian particle confined within a power-law trapping potential by following the trajectory of the particle that itself is translating linearly along one dimension with constant acceleration in a viscous fluid. Considered herein is an idealized version of this model, in that it is assumed that the force of the trapping potential is only felt by the translating Brownian particle confined within the trap, and that this Brownian particle moves relative to the fluid molecules that are held stationary. The results presented herein show that the transient fluctuation theorem applies not only to equilibrium steady-state distributions but also to nonequilibrium steady-state distributions of an ideal colloidal system in an accelerated frame of reference in the asymptotic (long-time) limit.

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“…Due to the cumulative contributions of physicists and mathematicians, such as Nikolai Lobachevsky (1792–1856), Hendrik Antoon Lorentz (1853–1928), Jules Henri Poincaré (1854–1912), Max Karl Ernst Ludwig Plank (1858–1947), Hermann Minkowski (1864–1909), Marie Salomea Skłodowska Curie (1867–1934), Albert Einstein (1879–1955), Amalie Emmy Noether (1882–1935), Erwin Rudolf Josef Alexander Schrödinger (1887–1861), Wolfgang Ernst Pauli (1900–1958), Werner Karl Heisenberg (1901–1976), and Paul Adrien Maurice Dirac (1902–1984), the concept of space experienced a dramatic transformation, from the classical Euclidean to the modern space-time continuum, reflecting the significance of the chirality concept [ 103 , 104 , 105 ]. In parallel, the enormous progress in our understanding of the significance of molecular chirality was made by Jean-Baptiste Biot (1774–1862), Louis Pasteur (1822–1895), Joseph Achille Le Bel (1847–1930), Jacobus Henricus van’t Hoff (1852–1911), Hermann Emil Louis Fisher (1852–1919), and many others.…”

Section: Epiloguementioning

confidence: 99%

“…As a result, it becomes clear that chirality, entropy, and energy are entangled parameters of the physical and chemical objects driving their spatial behavior, playing particularly important roles in protein folding and structural dynamics. The entropy of the bio-molecular system can be partitioned into energy-dependent components: translational, rotational, orientational, and vibrational [ 105 ]. It is notable that PhTs between enzyme functional states are usually connected to conformational changes, involving electron or proton transport (spin transport) and directional shifts of a group of atoms.…”

Section: Epiloguementioning

confidence: 99%

Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality

Dyakin

Uversky

2022

IJMS

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Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.

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Role of Entropy in Colloidal Self-Assembly

Cited by 25 publications

References 110 publications

Dynamic structural adaptations enable the endobiotic predation ofbdellovibrio bacteriovorus

Dynamic structural adaptations enable the endobiotic predation ofbdellovibrio bacteriovorus

A Theoretical Analysis of the Transient Fluctuation Theorem for Accelerated Colloidal Systems in the Long-Time Limit

Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality

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