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Abstract Although molecular vibronic spectra generation is pivotal for chemical analysis, tackling such exponentially complex tasks on classical computers remains inefficient. Quantum simulation, though theoretically promising, faces technological challenges in experimentally extracting vibronic spectra for molecules with multiple modes. Here, we propose a nontrivial algorithm to generate the vibronic spectra using states with zero displacements (squeezed vacuum states) coupled to a linear optical network, offering ease of experimental implementation. We also fabricate an integrated quantum photonic microprocessor chip as a versatile simulation platform containing 16 modes of single-mode squeezed vacuum states and a fully programmable interferometer network. Molecular vibronic spectra of formic acid and thymine under the Condon approximation are simulated using the quantum microprocessor chip with high reconstructed fidelity ( > 92%). Furthermore, vibronic spectra of naphthalene, phenanthrene, and benzene under the non-Condon approximation are also experimentally simulated. Such demonstrations could pave the way for solving complicated quantum chemistry problems involving vibronic spectra and computational tasks beyond the reach of classical computers.

The following theses are claimed, several contrasting current climate policies and taxonomies. Analysis, based on solely carbon dioxide emission and energy budget, concludes a set of concrete solutions for mitigating climate change effects. Some of the theses violate more orthodox policy which is thus protested against in order to move forward. •Our long-term goal must be to stop using all carbon-containing fuels, including natural gas and other fossil products as well as biofuels. •We must electrify society and industry, with electricity from only non-carbon-based power including nuclear power, hydro-electric, wind and solar power. •We must prepare ourselves for changes. Even if the present emission volumes of carbon dioxide were possible to stop immediately, various lag effects are inevitable and negative development will therefore continue for considerable time. •We must count with continued melting of land ice, the complete liquifying of the Antarctica ice expected to lead to a global sea level rise by some 60 m, flooding most capitals. Among various solutions to mitigate the effects of ice melting, including lowered global temperatures, the following is proposed. •To mitigate sea level rise, stationary water reservoirs should be built around the world. With estimated melting rates it would require ca 1 million reservoirs be deployed or expanded during the next 20-40 years. •Such reservoirs could also solve the emergent problem of lack of fresh water in many places. They could also be used for local storage of hydroelectric energy by using pump storage hydroelectric (PSH) technology. •All energy production sources should be analyzed according to a Total Balanced Energy Budget (TBEB) with the main objective of minimizing the emissions of greenhouse gases. •For each region/country, a table of available or conceivable complementary electric energy sources should be made and ranked according to TBEB—the sources given priority weights depending on feasibility, significance, and environmental friendliness. Tables are presented for Sweden, Norway, Denmark, Germany, France, Ukraine, California, Massachusetts, Maine, Peru, Australia, China and Japan. Generally, we find the following rank of priority applicable. •Solar energy from desert arid areas is given highest priority in replacing carbon-based forms of energy. Submarine electric cables may be deployed along the Australia-Singapore model, if the available power grids are insufficient for the energy transport. •Electrolysis of water producing clean hydrogen gas is given very high priorityboth for using hydrogen as fuel as well as for energy storage. Improved efficiency should be achieved by the development of electrolysis catalysts. •Hydroelectric power in combination with PSH is given high priority to mitigate both grid power fluctuations as well as source (solar and wind) intermittence. •False hope should not be seeded among society and politicians by inflating projects that are less realistic or suboptimal for technological, economic or other reasons. Here, probably most forms of “biofuels” (which although being “carbon neutral” do produce carbon dioxide) and “carbon capture” (catching carbon dioxide gas at the combustion site, compressing it to liquid and depositing it in salt mines or empty oil fields) are considered less significant compared to other more direct solutions. Both biofuels and carbon capture may be associated with social and environmental issues. •Political legislation and instruments (“taxonomy”) invented with the original objective of mitigating negative climate change effects should be reanalyzed and changed if not functional. The EU Emissions Trading System (EU ETS)—a market for outlet rights, for example, is a local initiative which despite its valuable ambition might be suboptimal with respect to goal of efficient decrease of carbon dioxide emission globally. Similarly, “climate taxonomy” can create loopholes bypassing a sound TBEB. •Science-based targets (SBT) to decarbonize the private sector as part of global efforts to achieve the temperature goal of the Paris Agreement should be further encouraged. •Solve economic and political challenges allowing and promoting establishment of required international energy collaborations (e.g., for solar energy cross-continental transport programs).

The molea concept and Avogadro’s number are discussed as sought by Albert Einstein in his PhD thesis of 1905. Einstein would probably have regarded the metric system of units based on centimetre-gram-second (cgs) preferable to today’s SI system and specifically he would have rejected a recent SI suggestion to redefine Avogadro’s constant as based on a nonatomistic continuum description of matter. He would probably also have preferred keeping a dualistic definition of mole able of bookkeeping both mass and number of particles: we advocate that here and call it the ‘Einstein Definition’ and as Avogadro’s number we shall adopt an integer, the cube of 84446888 as suggested by Fox and Hill, providing also a definition of the kilogram based on the atomic mass of the carbon 12 isotope. Einstein was the first to explain the microscopic movements of pollen grains reported by Robert Brown in 1828 and his explanation that the particles move as a result of an unequal number of water molecules bumping into them from opposite sides was what finally made the scientific world accept the atom theory in its modern shape. In a cosmic diffusion analogy, pollen or bacterial spores moving randomly in outer space driven by the solar winds between solar systems can be envisaged. Applying Einstein’s diffusion theory, one can argue that life might have emerged from far outside of our planet from billions of solar systems, though not from outside of our Milky Way galaxy. As a curiosity we note that the number of solar systems (stars) in the Universe has been estimated to be of the order of Avogadro’s number. aEtymology: “Mole” was derived from French Molécule (extremely small particle) or diminutive from Greek [Formula: see text] (molos= substance). In analogy with atom, derived from Greek atomos or atemnein, uncleavable, we may thus interpret molecule as the smallest part that a substance can be divided into without losing its chemical character.

The behavior of benzoic acid in polyethylene inspired me to reflect on why water is a unique molecule that all living organisms depend upon. From properties of DNA in aqueous solution a seemingly counter-intuitive conjecture emerges: water is needed for the creation of certain dry low-dielectric nm-size environments where hydrogen bonding exerts strong recognition power. Such environments seem to be functionally crucial, and their interactions with other hydrophobic environments, or with hydrophobic agents that modulate the chemical potential of water, can cause structural transformations via ‘hydrophobic catalysis’. Possibly combined with an excluded volume osmosis effect (EVO), hydrophobic catalysis may have important biological roles, e.g., in genetic recombination. Hydrophobic agents are found to strongly accelerate spontaneous DNA strand exchange as well as certain other DNA rearrangement reactions. It is hypothesized that hydrophobic catalysis be involved in gene recognition and gene recombination mediated by bacterial RecA (one of the oldest proteins we know of) as well as in sexual recombination in higher organisms, by Rad51. Hydrophobically catalyzed unstacking fluctuations of DNA bases can favor elongated conformations, such as the recently proposed Σ-DNA, with potential regulatory roles. That living cells can survive as dormant spores, with very low water content and in principle as such travel far in space is reflected upon: a random walk model with solar photon pressure as driving force indicates our life on earth could not have originated outside our galaxy but possibly from many solar systems within it — at some place, though, where there was plenty of liquid water.

The human protein Rad51 is double-edged in cancer contexts: on one hand, preventing tumourigenesis by eliminating potentially carcinogenic DNA damage and, on the other, promoting tumours by introducing new mutations. Understanding mechanistic details of Rad51 in homologous recombination (HR) and repair could facilitate design of novel methods, including CRISPR, for Rad51-targeted cancer treatment. Despite extensive research, however, we do not yet understand the mechanism of HR in sufficient detail, partly due to complexity, a large number of Rad51 protein units being involved in the exchange of long DNA segments. Another reason for lack of understanding could be that current recognition models of DNA interactions focus only on hydrogen bond-directed base pair formation. A more complete model may need to include, for example, the kinetic effects of DNA base stacking and unstacking (‘longitudinal breathing’). These might explain how Rad51 can recognize sequence identity of DNA over several bases long stretches with high accuracy, despite the fact that a single base mismatch could be tolerated if we consider only the hydrogen bond energy. We here propose that certain specific hydrophobic effects, recently discovered destabilizing stacking of nucleobases, may play a central role in this context for the function of Rad51.

Formulas derived from theoretical physics provide important insights about the nematocyst discharge process of Cnidaria (Hydra, jellyfishes, box-jellyfishes and sea-anemones). Our model description of the fastest process in living nature raises and answers questions related to the material properties of the cell- and tubule-walls of nematocysts including their polysialic acid (polySia) dependent target function. Since a number of tumor-cells, especially brain-tumor cells such as neuroblastoma tissues carry the polysaccharide chain polySia in similar concentration as fish eggs or fish skin, it makes sense to use these findings for new diagnostic and therapeutic approaches in the field of nanomedicine. Therefore, the nematocyst discharge process can be considered as a bionic blue-print for future nanomedical devices in cancer diagnostics and therapies. This approach is promising because the physical background of this process can be described in a sufficient way with formulas presented here. Additionally, we discuss biophysical and biochemical experiments which will allow us to define proper boundary conditions in order to support our theoretical model approach. PolySia glycans occur in a similar density on malignant tumor cells than on the cell surfaces of Cnidarian predators and preys. The knowledge of the polySia-dependent initiation of the nematocyst discharge process in an intact nematocyte is an essential prerequisite regarding the further development of target-directed nanomedical devices for diagnostic and therapeutic purposes. The theoretical description as well as the computationally and experimentally derived results about the biophysical and biochemical parameters can contribute to a proper design of anti-tumor drug ejecting vessels which use a stylet-tubule system. Especially, the role of nematogalectins is of interest because these bridging proteins contribute as well as special collagen fibers to the elastic band properties. The basic concepts of the nematocyst discharge process inside the tubule cell walls of nematocysts were studied in jellyfishes and in Hydra which are ideal model organisms. Hydra has already been chosen by Alan Turing in order to figure out how the chemical basis of morphogenesis can be described in a fundamental way. This encouraged us to discuss the action of nematocysts in relation to morphological aspects and material requirements. Using these insights, it is now possible to discuss natural and artificial nematocyst-like vessels with optimized properties for a diagnostic and therapeutic use, e.g., in neurooncology. We show here that crucial physical parameters such as pressure thresholds and elasticity properties during the nematocyst discharge process can be described in a consistent and satisfactory way with an impact on the construction of new nanomedical devices.

Background: Oct4 is a transcription factor that plays a major role for the preservation of the pluripotent state in embryonic stem cells as well as for efficient reprogramming of somatic cells to induced pluripotent stem cells (iPSC) or other progenitors. Protein-based reprogramming methods mainly rely on the addition of a fused cell penetrating peptide. This study describes that Oct4 inherently carries a protein transduction domain, which can translocate into human and mouse cells. Results: A 16 amino acid peptide representing the third helix of the human Oct4 homeodomain, referred to as Oct4 protein transduction domain (Oct4-PTD), can internalize in mammalian cells upon conjugation to a fluorescence moiety thereby acting as a cell penetrating peptide (CPP). The cellular distribution of Oct4-PTD shows diffuse cytosolic and nuclear staining, whereas penetratin is strictly localized to a punctuate pattern in the cytoplasm. By using a Cre/loxP-based reporter system, we show that this peptide also drives translocation of a functionally active Oct4-PTD-Cre-fusion protein. We further provide evidence for translocation of full length Oct4 into human and mouse cell lines without the addition of any kind of cationic fusion tag. Finally, physico-chemical properties of the novel CPP are characterized, showing that in contrast to penetratin a helical structure of Oct4-PTD is only observed if the FITC label is present on the N-terminus of the peptide. Conclusions: Oct4 is a key transcription factor in stem cell research and cellular reprogramming. Since it has been shown that recombinant Oct4 fused to a cationic fusion tag can drive generation of iPSCs, our finding might contribute to further development of protein-based methods to generate iPSCs. Moreover, our data support the idea that transcription factors might be part of an alternative paracrine signalling pathway, where the proteins are transferred to neighbouring cells thereby actively changing the behaviour of the recipient cell.

This article presents a new design of flow-orientation device for the study of bio-macromolecules, including DNA and protein complexes, as well as aggregates such as amyloid fibrils and liposome membranes, using Linear Dichroism (LD) spectroscopy. The design provides a number of technical advantages that should make the device inexpensive to manufacture, easier to use and more reliable than existing techniques. The degree of orientation achieved is of the same order of magnitude as that of the commonly used concentric cylinders Couette flow cell, however, since the device exploits a set of flat strain-free quartz plates, a number of problems associated with refraction and birefringence of light are eliminated, increasing the sensitivity and accuracy of measurement. The device provides similar shear rates to those of the Couette cell but is superior in that the shear rate is constant across the gap. Other major advantages of the design is the possibility to change parts and vary sample volume and path length easily and at a low cost. [ABSTRACT FROM AUTHOR]

DNA strand exchange is of great importance in vivo for genetic recombination and DNA repair. The detailed mechanism of strand exchange is not understood in full detail despite extensive studies. Simplistic model systems in which molecular parameters can be varied independently are therefore of interest to study. We chose the surface of a positively charged liposome as a scaffold, which we recently demonstrated to be able to catalyze the exchange of fully complementary DNA oligonucleotides. We here study how single base pair mismatches affect the rate of strand exchange on the liposome surface. Interestingly, the rate of the exchange does not simply follow the stability of the duplex in solution, as determined by melting temperatures, but also depends sensitively on the position of the mismatch. For duplexes with similar melting temperatures, the exchange is much faster for a mismatch close to the end than for a mismatch in the middle of the sequence. Our results suggest that the single strands are stabilized by the liposome surface; therefore, the duplex is fraying more and the DNA opens up in a zipperlike fashion on the surface, increasing the probability of strand exchange. We also show that the competition between greater stability (higher Tmin solution) and higher concentration is important for the final composition of the duplex when a large excess of single strands is added to a complementary double-stranded DNA. Finally, the similar exchange rate constants for fully base-paired duplexes on the liposome surface when adding fully matched single strands or single strands with a mismatched base indicate that the rate is governed largely by separation of the initial duplex and not by the formation of the product duplex. [ABSTRACT FROM AUTHOR]

In various chemical systems enthalpy−entropy compensation (EEC) is a well-known rule of behavior, although the physical roots of it are still not completely understood. It has been frequently questioned whether EEC is a truly physical phenomenon or a coincidence due to trivial mathematical connections between statistical-mechanical parameters or even simpler, a phantom effect resulting from the misinterpretation of experimental data. Here, we review EEC from a new standpoint and conclude that it may be rationalized in terms of hidden but physically real factors implying a Carnot-cycle model in which a micro-phase transition (MPT) plays a crucial role. Examples of such MPTs underlying physically valid EEC should be typically cooperative processes in supramolecular aggregates, like changes of structured water at hydrophobic surfaces, conformational transitions upon ligand-biopolymer binding, and so forth. The MPT notion could help rationalize the occurrence of EEC in connection with hydration and folding of proteins, functioning of molecular motors, and similar phenomena. [ABSTRACT FROM AUTHOR]

Systematical differential calorimetry experiments on DNA oligomers with different lengths and placed in water solutions with various added salt concentrations may, in principle, unravel important information about the structure and dynamics of the DNA and their water−counterion surrounding. With this in mind, to reinterpret the most recent results of calorimetric experiments on DNA oligomers of such a kind, the recent enthalpy−entropy compensation theory has been used. It is demonstrated that the application of the latter could enable direct estimation of thermodynamic parameters of the microphase transitions connected to the changes in DNA dynamical regimes versus the length of the biopolymers and the ionic strengths of their water solutions, and this calls for much more systematical experimental and theoretical studies in this field. [ABSTRACT FROM AUTHOR]