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All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes initiation, elongation, termination, and recycling. In fact, peptide bonds are formed only during the elongation phase, which comprises periodic association of transfer RNAs and multiple auxiliary proteins with the ribosome and the addition of an amino acid to the nascent polypeptide one at a time. The protein spends a considerable amount of time attached to the ribosome. Here, we conceptually divide this portion of the protein lifetime into three stages. We define each stage on the basis of the position of the N-terminus of the nascent polypeptide within the ribosome exit tunnel and the context of the catalytic center. We argue that nascent polypeptides experience a variety of forces that determine how they translocate through the tunnel and interact with the tunnel walls. We review current knowledge about nascent polypeptide translocation and identify several white spots in our understanding of the birth of proteins., Comment: 19 pages, 3 figures

Bosonic systems with negative Wigner function superposition states are fundamentally witnessing nonlinear quantum dynamics beyond linearized systems and, recently, have become essential resources of quantum technology with many applications. Typically, they appear due to sophisticated combination of external drives, nonlinear control, measurements or strong nonlinear dissipation of subsystems to an environment. Here, we propose a conceptually different and more autonomous way to obtain such states, avoiding these ingredients, using purely sudden interaction decay in the paradigmatic interacting qubit-oscillator system weakly coupled to bath at thermal equilibrium in a low-temperature limit. We demonstrate simultaneously detectable unconditional negative Wigner function and quantum coherence and their qualitative enhancement employing more qubits., Comment: Accepted to Quantum

In living organisms, proteins and peptides are often under the influence of mechanical forces, especially in confined spaces such as membrane channels, ribosome exit tunnel, or proteasome gate. Due to the directional nature of proteins as polymers with distinct ends, forces have the potential to influence protein conformational dynamics in a direction-dependent manner. In this study, we employed force-probe molecular dynamics simulations to investigate the impact of pulling a peptide through a confined environment versus pushing it in the same direction. Our model involves a carbon nanotube and one of three decapeptides with varying amino acid sequences. The simulations reveal that the difference between pulling the C-terminus and pushing the N-terminus is relatively minor when considering the conformational ensembles of the peptides. The loading rate of the force probe and the amino acid sequence of the peptide play a more important role. However, the application of force to the peptide significantly influences the relative motion of the peptides with respect to the nanotube. Pulling the peptide results in a smoother translocation through the nanotube compared to pushing, although the internal conformational dynamics of the peptide add complexity in either case. Our findings shed light on how short peptides navigate confined spaces within the cellular environment, emphasizing the importance of force-probe simulation studies in understanding these processes., Comment: 16 pages, 8 figures, added GitHub repo, updated Acknowledgment

Quantum coherence represented by a superposition of energy eigenstates is, together with energy, an important resource for quantum technology and thermodynamics. Energy and quantum coherence however, can be complementary. The increase of energy can reduce quantum coherence and vice versa. Recently, it was realized that steady-state quantum coherence could be autonomously harnessed from a cold environment. We propose a conditional synthesis of $N$ independent two-level systems (TLS) with partial quantum coherence obtained from an environment to one coherent system using a measurement able to increase both energy and coherence simultaneously. The measurement process acts here as a Maxwell demon synthesizing the coherent energy of individual TLS to one large coherent quantum battery. The measurement process described by POVM elements is diagonal in energy representation and, therefore, it does not project on states with quantum coherence at all. We discuss various strategies and their efficiency to reach large coherent energy of the battery. After numerical optimization and proof-of-principle tests, it opens way to feasible repeat-until-success synthesis of coherent quantum batteries from steady-state autonomous coherence.

Quantum coherent superpositions of states with different energies, i.e., states with coherence with respect to energy basis, are important resource for modern quantum technologies. States with small coherence can be obtained either autonomously, due to the effect of a weak coherent drive or, potentially, due to the presence of an environment. In this paper, we propose a measurement-based protocol for quantum coherence synthesis from individual systems (with low initial coherence) into a global (and higher) coherence of the joint system. As an input, it uses $N$ non-interacting copies of two-level systems (TLS), with low initial energy and coherence. These can be supplied by, e.g., a weak external drive or can result from an interaction with a bath. This protocol conditionally synthesizes an output state with higher energy and coherence than the initial state had, representing an universal process whose rules have not been well studied, yet. In addition to energy and coherence, we study the quantity called mutual coherence, showing increase after the protocol application, as well. This approach is based on application of sequential pairwise projective measurements on TLS pairs (conditionally removing their ground states), that are diagonal in the TLS energy basis. The functionality of the coherence synthesis is robust with respect to dephasing effects of the TLS environment on the system. Our approach may show its benefits in quantum sensing, quantum batteries charging, or other applications where synthesis of a larger coherent system from smaller (weaker) resources is useful., Comment: 13 pages, 8 figures

Quantum superposition of energy eigenstates can appear autonomously in a single quantum two-level system coupled to a low-temperature thermal bath, if such coupling has a proper composite nature. We propose here a principally different and more feasible approach employing engineered interactions between two-level systems being thermalized into a global Gibbs state by weakly coupled thermal bath at temperature $T$. Therefore, in such case quantum coherence appears by a different mechanism, whereas the system-bath coupling does not have to be engineered. We demonstrate such autonomous coherence generation reaching maximum values of coherence. Moreover, it can be alternatively built up by using weaker but collective interaction with several two-level systems. This approach surpasses the coherence generated by the engineered system-bath coupling for comparable interaction strengths and directly reduces phase estimation error in quantum sensing. This represents a necessary step towards the autonomous quantum sensing., Comment: 10 pages, 4 figures

Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the $\sigma$-hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the $\sigma$-hole is often modeled as a pseudo-atom with a positive partial charge located off the halogen nucleus. Here we address a question, to what extent the pseudo-atom affects partial charges of other atoms in the molecule. To this aim, we have thoroughly analyzed partial charges of over 2300 halogenated molecules from the ZINC database calculated by the Restricted Electrostatic Potential (RESP) method and compared them with the charges fitted by RESP including the pseudo-atom. We show that the pseudo-atom improves charge fitting for a vast majority of molecules. The $\sigma$-hole, modeled as the off-center charge, affects the atoms within three covalent bonds from the halogen., Comment: 11 pages, 3 figures

We theoretically and experimentally investigate conditional enhancement of overall coherence of quantum states by probabilistic quantum operations that apply to the input state a quantum filter diagonal in the basis of incoherent states. We identify the optimal filters that for a given probability of successful filtering maximize the output coherence. We verify the performance of the studied quantum filters in a proof-of-principle experiment with linear optics, where a pair of two-level quantum systems is represented by polarization states of two photons. We comprehensively characterize the implemented two-qubit linear optical quantum filters by full quantum process tomography and we experimentally observe the optimal quantum coherence enhancement by quantum filtering., Comment: 10 pages, 7 figures

The proteasome is a large biomolecular complex responsible for protein degradation. It is under intense research due to its fundamental role in cellular homeostasis, and tremendous potential for medicinal applications. Recent data from X-ray crystallography and cryo-electron microscopy have suggested that there is a large-scale structural change upon binding of an inhibitor. We carried out atomistic molecular dynamics simulations of the native and inhibited proteasomes to understand the molecular details of the inhibition. Here we describe the technical details of the simulations and assess the quality of the trajectories obtained. The biochemical aspects of the proteasome are under further investigation and will be published elsewhere. This work was a part of the GCS-Prot project at the HLRS, run on the Cray XC40 supercomputing system., Comment: 11 pages, 8 figures, to be published in High Performance Computing in Science & Engineering 2020

The appearance of steady-state coherence (SSC) from system-bath interaction proves that quantum effects can appear without an external drive. Such SSC could become a resource to demonstrate quantum advantage in the applications. We predict the generation of SSC if the target system repeatedly interacts with independent and non-correlated bath elements. To describe their behavior, we use the collision model approach of system-bath interaction, where the system interacts with one bath element (initially in an incoherent state) at a time, asymptotically (in the fast-collision regime) mimicking a macroscopic Markovian bath coupled to the target system. Therefore, the SSC qualitatively appears to be the same as if the continuous Markovian bath would be used. We confirm that the presence of composite system-bath interactions under the rotating-wave approximation (RWA) is the necessary condition for the generation of SSC using thermal resources in collision models. Remarkably, we show that SSC substantially increases if the target system interacts collectively with more than one bath element at a time. Already few bath elements collectively interacting with the target system are sufficient to increase SSC at non-zero temperatures at the cost of tolerable lowering the final state purity. From the thermodynamic perspective, the SSC generation in our collision models is inevitably linked to a non zero power input (and thus heat dissipated to the bath) necessary to reach the steady-state, although such energetic cost can be lower compared to cases relying on SSC non generating interactions., Comment: 19 pages, 6 figures. Two columns. Close to the published version

Halogen bond (X-bond) is a noncovalent interaction between a halogen atom and an electron donor. It is often rationalized by a region of the positive electrostatic potential on the halogen atom, so-called $\sigma$-hole. The X-bond strength increases with the atomic number of the halogen involved, thus for heavier halogens, relativistic effects become of concern. This poses a challenge for the quantum chemical description of X-bonded complexes. To quantify scalar relativistic effects (SREs) on the interaction energies and $\sigma$-hole properties, we have performed highly accurate coupled-cluster calculations at the complete basis set limit of several X-bonded complexes and their halogenated monomers. The SREs turned to be comparable in magnitude to the effect of basis set. The nonrelativistic calculations typically underestimate the attraction by up to 5% or 23% for brominated and iodinated complexes, respectively. Counter-intuitively, the electron densities at the bond critical points are larger for SRE-free calculations than for the relativistic ones. SREs yield smaller, flatter, and more positive $\sigma$-holes. Finally, we highlight the importance of diffuse functions in the basis sets and provide quantitative arguments for using basis sets with pseudopotentials as an affordable alternative to a more rigorous Douglas-Kroll-Hess relativistic theory., Comment: 21 pages including Suppl. Info, 8 figures, revised version, added bond critical points, changed authors order

Coherent quantum oscillators are basic physical systems both in quantum statistical physics and quantum thermodynamics. Their realizations in lab often involve solid-state devices sensitive to changes in ambient temperature. We represent states of the solid-state optomechanical oscillator with temperature-dependent frequency by equivalent states of the mechanical oscillator with temperature-dependent energy levels. We interpret the temperature dependence as a consequence of strong coupling between the oscillator and the heat bath. We explore parameter regimes corresponding to anomalous behavior of mechanical and thermodynamic characteristics as a consequence of the strong coupling: (i) The localization and the purification induced by heating, and (ii) the negativity of two generalized heat capacities. The capacities can be used to witness non-linearity in the temperature dependency of the energy levels. Our phenomenological experimentally-oriented approach can stimulate development of new optomechanical and thermomechanical experiments exploring basic concepts of strong coupling thermodynamics., Comment: 14 pages, 5 figures, references added, new style, changes in the text, corrected typos

We identify sufficient conditions on the structure of the interaction Hamiltonian between a two-level quantum system and a thermal bath which, without any external drive or coherent measurement, guarantee the generation of steady-state coherences (SSC). The SSC this way obtained remarkably turn out to be independent on the initial state of the system, which therefore could be even taken initially incoherent. We characterize in detail this phenomenon first analytically in the weak coupling regime for two paradigmatic models, and then numerically in more complex systems without any assumption on the coupling strength. In all these cases we find that SSC become increasingly significant as the bath is cooled down. These results can be therefore directly verified in many experimental platforms., Comment: Accepted version in Physical Review Letters. 4 pages (and 2 figures) of main text + 28 pages (and 7 figures) of Supplementary Material

The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM), the structure of the ribosome was resolved at atomic resolution in many functional and conformational states. Molecular dynamics simulations have added information on dynamics and energetics to the available structural information, thereby have bridged the gap to the kinetics obtained from single-molecule and bulk experiments. Here, we review recent computational studies that brought notable insights into ribosomal structure and function., Comment: 11 pages, 3 figures, to be published in Current Opinion in Structural Biology

To contribute to the understanding of noncovalent binding of halogenated molecules with a biological activity, electrostatic potential (ESP) maps of more than 2,500 compounds were thoroughly analysed. A peculiar region of positive ESP, called $\sigma$-hole, is a concept of central importance for halogen bonding. We aim at simplifying the view on $\sigma$-holes and provide general trends in organic drug-like molecules. The results are in fair agreement with crystallographic surveys of small molecules as well as of biomolecular complexes and attempt to improve the intuition of chemists when dealing with halogenated compounds., Comment: 5 pages, 3 figures, published

Halogen bonding (X-bonding) has attracted notable attention among noncovalent interactions. This highly directional attraction between a halogen atom and an electron donor has been exploited in knowledge-based drug design. A great deal of information has been gathered about X-bonds in protein-ligand complexes, as opposed to nucleic acid complexes. Here we provide a thorough analysis of nucleic acid complexes containing either halogenated building blocks or halogenated ligands. We analyzed close contacts between halogens and electron-rich moieties. The phosphate backbone oxygen is clearly the most common halogen acceptor. We identified 21 X-bonds within known structures of nucleic acid complexes. A vast majority of the X-bonds is formed by halogenated nucleobases, such as bromouridine, and feature excellent geometries. Noncovalent ligands have been found to form only interactions with suboptimal interaction geometries. Hence, the first X-bonded nucleic acid binder remains to be discovered., Comment: 19 pages, 12, figures, published

In the field of noncovalent interactions a new paradigm has recently become popular. It stems from the analysis of molecular electrostatic potentials and introduces a label, which has recently attracted enormous attention. The label is {\sigma}-hole, and it was first used in connection with halogens. It initiated a renaissance of interest in halogenated compounds, and later on, when found also on other groups of atoms (chalcogens, pnicogens, tetrels and aerogens), it resulted in a new direction of research of intermolecular interactions. In this review, we summarize advances from about the last 10 years in understanding those interactions related to {\sigma}-hole. We pay particular attention to theoretical and computational techniques, which play a crucial role in the field., Comment: 111 pages, 22 figures, published

A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general., Comment: 45 pages, 20 figures, published, added Supplementary information

We propose a generation of a low-noise state of optomechanical oscillator by a temperature dependent force. We analyze the situation in which a quantum optomechanical oscillator (denoted as the membrane) is driven by an external force (produced by the piston). Both systems are embedded in a common heat bath at certain temperature $T$. The driving force the piston exerts on the membrane is bath temperature dependent. Initially, for $T=T_0$, the piston is linearly coupled to the membrane. The bath temperature is then reversibly changed to $T\neq T_0$. The change of temperature shifts the membrane, but simultaneously also increases its fluctuations. The resulting equilibrium state of the membrane is analyzed from the point of view of mechanical, as well as of thermodynamic characteristics. We compare these characteristics of membrane and derive their intimate connection. Next, we cool down the thermal noise of the membrane, bringing it out of equilibrium, still being in the contact with heat bath. This cooling retains the effective canonical Gibbs state with the effective temperature $T^\star$. In such case we study the analogs of the equilibrium quantities for low-noise mechanical states of the membrane.

We examine the dynamics of circulating modes of a Bose-Einstein condensate confined in toroidal lattice. Nonlinearity due to interactions leads to criticality that separates oscillatory and self-trapped phases among counter-propagating modes which however share the same physical space. In the mean-field limit, the criticality is found to substantially enhance sensitivity to rotation of the system. Analysis of the quantum dynamics reveals the fluctuations near criticality are significant, that we explain using spin-squeezing formalism visualized on a Bloch sphere. We utilize the squeezing to propose a Ramsey interferometric scheme that suppresses fluctuation in the relevant quadrature sensitive to rotation., Comment: 11 pages, 9 figures (Fig. 9 resolution reduced to meet size limits)

We propose a scheme for spin-squeezing in the orbital motion of a Bose-Einstein condensate (BEC) in a toroidal trap. A circular lattice couples two counter-rotating modes and squeezing is generated by the nonlinear interaction spatially modulated at half the lattice period. By varying the amplitude and phase of the modulation, various cases of the twisting tensor can be directly realized, leading to different squeezing regimes. These include one-axis twisting and the two-axis counter-twisting which are often discussed as the most important paradigms for spin squeezing. Our scheme naturally realizes the Lipkin-Meshkov-Glick model with the freedom to vary all its parameters simultaneously., Comment: 9 pages, 6 figures, to appear in PRA

A minimal model of a quantum refrigerator (QR), i.e. a periodically phase-flipped two-level system permanently coupled to a finite-capacity bath (cold bath) and an infinite heat dump (hot bath), is introduced and used to investigate the cooling of the cold bath towards the absolute zero (T=0). Remarkably, the temperature scaling of the cold-bath cooling rate reveals that it does not vanish as T->0 for certain realistic quantized baths, e.g. phonons in strongly disordered media (fractons) or quantized spin-waves in ferromagnets (magnons). This result challenges Nernst's third-law formulation known as the unattainability principle.

Sequence alignment forms the basis of many methods for functional annotation by phylogenetic comparison, but becomes unreliable in the `twilight' regions of high sequence divergence and short gene length. Here we perform a cross-species comparison of two herpesviruses, VZV and KSHV, with a hybrid method called graph alignment. The method is based jointly on the similarity of protein interaction networks and on sequence similarity. In our alignment, we find open reading frames for which interaction similarity concurs with a low level of sequence similarity, thus confirming the evolutionary relationship. In addition, we find high levels of interaction similarity between open reading frames without any detectable sequence similarity. The functional predictions derived from this alignment are consistent with genomic position and gene expression data.

We predict that if internal and momentum states of an interfering object are correlated (entangled), then by measuring its internal state we may infer both path (corpuscular) and phase (wavelike) information with much higher precision than for objects lacking such entanglement. We thereby partly circumvent the standard complementarity constraints of which-path detection., Comment: 5 pages, 2 figures

Focusing on the optimization version of the random K-satisfiability problem, the MAX-K-SAT problem, we study the performance of the finite energy version of the Survey Propagation (SP) algorithm. We show that a simple (linear time) backtrack decimation strategy is sufficient to reach configurations well below the lower bound for the dynamic threshold energy and very close to the analytic prediction for the optimal ground states. A comparative numerical study on one of the most efficient local search procedures is also given., Comment: 12 pages, submitted to Phys. Rev. E, accepted for publication

We examine a model of biological evolution of Eigen's quasispecies in a holey fitness landscape, where the fitness of a site is either 0 (lethal site) or a uniform positive constant (viable site). So, the evolution dynamics is determined by the topology of the genome space. It is modeled by the random Bethe lattice. We use the effective medium and single-defect approximations to find the criteria, under which the localized quasispecies cloud is created. We find that shorter genomes, which are more robust to random mutations than average, represent a selective advantage which we call ``topological''. A way of assessing empirically the relative importance of reproductive success and topological advantage is suggested., Comment: 6 pages, 5 figures, svjour class, accepted in EPJ B

We compared the properties of the error threshold transition in quasispecies evolution for three different topologies of the genome space. They are a) hypercube b) rugged landscape modelled by an ultrametric space, and c) holey landscape modelled by Bethe lattice. In all studied topologies the phase transition exists. We calculated the critical exponents in all the cases. For the critical exponent corresponding to appropriately defined susceptibility we found super-universal value., Comment: 23 pages, 4 figures, accepted for publication in Physica A, LaTeX - elsart