Assessment of interatomic potentials for atomistic analysis of static and dynamic properties of screw dislocations in W

Screw dislocations in bcc metals display non-planar cores at zero temperature which result in high lattice friction and thermally activated strain rate behavior. In bcc W, electronic structure molecular statics calculations reveal a compact, non-degenerate core with an associated Peierls stress between 1.7 and 2.8 GPa. However, a full picture of the dynamic behavior of dislocations can only be gained by using more efficient atomistic simulations based on semiempirical interatomic potentials. In this paper we assess the suitability of five different potentials in terms of static properties relevant to screw dislocations in pure W. As well, we perform molecular dynamics simulations of stress-assisted glide using all five potentials to study the dynamic behavior of screw dislocations under shear stress. Dislocations are seen to display thermally-activated motion in most of the applied stress range, with a gradual transition to a viscous damping regime at high stresses. We find that one potential predicts a core transformation from compact to dissociated at finite temperature that affects the energetics of kink-pair production and impacts the mechanism of motion. We conclude that a modified embedded-atom potential achieves the best compromise in terms of static and dynamic screw dislocation properties, although at an expense of about ten-fold compared to central potentials

DFT Study of Planar Boron Sheets: A New Template for Hydrogen Storage

We study the hydrogen storage properties of planar boron sheets and compare them to those of graphene. The binding of molecular hydrogen to the boron sheet (0.05 eV) is stronger than that to graphene. We find that dispersion of alkali metal (AM = Li, Na, and K) atoms onto the boron sheet markedly increases hydrogen binding energies and storage capacities. The unique structure of the boron sheet presents a template for creating a stable lattice of strongly bonded metal atoms with a large nearest neighbor distance. In contrast, AM atoms dispersed on graphene tend to cluster to form a bulk metal. In particular the boron-Li system is found to be a good candidate for hydrogen storage purposes. In the fully loaded case this compound can contain up to 10.7 wt. % molecular hydrogen with an average binding energy of 0.15 eV/H2.Comment: 19 pages, 7 figures, and 3 table

Energy landscape of relaxed amorphous silicon

We analyze the structure of the energy landscape of a well-relaxed 1000-atom model of amorphous silicon using the activation-relaxation technique (ART nouveau). Generating more than 40,000 events starting from a single minimum, we find that activated mechanisms are local in nature, that they are distributed uniformly throughout the model and that the activation energy is limited by the cost of breaking one bond, independently of the complexity of the mechanism. The overall shape of the activation-energy-barrier distribution is also insensitive to the exact details of the configuration, indicating that well-relaxed configurations see essentially the same environment. These results underscore the localized nature of relaxation in this material.Comment: 8 pages, 12 figure

Surface and interstitial Ti diffusion at the rutile TiO2(110) surface

Diffusion of Ti through the TiO2 (110) rutile surface plays a key role in the growth and reactivity of TiO2. To understand the fundamental aspects of this important process, we present an analysis of the diffusion of Ti adspecies at the stoichiometric TiO2(110) surface using complementary computational methodologies of density functional theory corrected for on-site Coulomb interactions (DFT+U) and a charge equilibration (QEq) atomistic potential to identify minimum energy pathways. We find that diffusion of Ti from the surface to subsurface (and vice versa) follows an intersticialcy exchange mechanism, involving exchange of surface Ti with the 6-fold coordinated Ti below the bridging oxygen rows. Diffusion in the subsurface between layers also follows an interstitialcy mechanism. The diffusion of Ti is discussed in light of continued attempts to understand the re-oxidation of non-stoichiometric TiO2(110) surfaces

O(N) methods in electronic structure calculations

Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high performance computers. The linear scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas is then discussed. The applications of linear scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear scaling methods are discussed.Comment: 85 pages, 15 figures, 488 references. Resubmitted to Rep. Prog. Phys (small changes

Regionally reduced brain volume, altered serotonin neurochemistry, and abnormal behavior in mice null for the circadian rhythm output gene Magel2.

Magel2 belongs to the MAGE/necdin family of proteins, which have roles in cell cycle, differentiation, and apoptosis. The Magel2 gene is expressed in various brain regions, most notably the hypothalamus. Mice with a targeted deletion of Magel2 display hypoactivity, blunted circadian rhythm, decreased fertility, and increased adiposity. The human ortholog, MAGEL2, is one of a set of paternally expressed, imprinted genes inactivated in most cases of Prader-Willi syndrome, a complex neurodevelopmental disorder. To explore the role of Magel2, brain morphology, brain neurochemistry, and behavior were measured in Magel2-null mice. Brain volume was reduced in specific regions, particularly in the parieto-temporal lobe of the cerebral cortex, the amygdala, the hippocampus, and the nucleus accumbens, as measured by quantitative magnetic resonance imaging. Abnormal neurochemistry was detected in brain samples from adult mice, consisting of decreased serotonin and 5-hydroxyindoleacetic acid in the cortex and the hypothalamus, and decreased dopamine in the hypothalamus. Magel2-null mice displayed relatively normal motor and learning abilities, but exhibited abnormal behavior in novel environments. This study lends support to the important role of the circadian rhythm output gene Magel2 in brain structure and behavior. Ó 2009 Wiley-Liss, Inc. Key words: Prader-Willi syndrome; anxiety; magnetic resonance imaging; circadian rhythm; imprinting INTRODUCTION Magel2 is a member of the Type II melanoma-associated antigen gene (MAGE) protein family, which share a protein-protein interaction domain called the MAGE homology/conserved domain 1085 Neuropsychiatric Genetics 1995]. The MAGE homology domain of several Type II MAGE proteins (necdin, MAGE-G1, MAGED1) binds to multiple transmembrane receptors involved in intracellular signaling MAGEL2 and NDN, the gene that encodes the MAGE protein necdin, are among a small set of genes that are typically inactivated in Prader-Willi syndrome (PWS). PWS is a congenital disorder characterized by symptoms of varying severity among affected individuals: intellectual disability, hypotonia, short stature, childhood-onset hyperphagia often leading to obesity, excessive sleepiness, neuroendocrine abnormalities, and incomplete sexual development We recently described a mouse strain carrying a gene-targeted lacZ insertion into the Magel2 locus, creating a null Magel2 allele MATERIALS AND METHODS Magel2-Null Mice All animal studies were conducted in accordance with the Canadian Council on Animal Care Guidelines and Policies with approval from the local Animal Policy and Welfare Committees. Magel2-null mice carry a replacement of the Magel2 gene with a LacZ reporter cassette, resulting in complete loss of Magel2 function in heterozygotes with a paternally derived gene-targeted allele Sample Preparation for MRI Magel2-null mice (n ¼ 6) and their wild-type littermates (n ¼ 6) were anesthetized at 26 weeks of age with a combination of Ketamine (100 mg/kg, Pfizer, Kirkland, QC, Canada) and Rompun (20 mg/kg, Bayer, Inc., Toronto, ON, Canada) via intraperitoneal injection. A previously described sample preparation protocol for scanning was used with slight modifications MRI Image Acquisition A multi-channel 7.0-T MRI scanner (Varian, Inc., Palo Alto, CA) with a 6 cm inner bore diameter insert gradient set was used to acquire anatomical images of brains within skulls. Prior to imaging, the samples were removed from the contrast agent solution, blotted and placed into 13 mm diameter plastic tubes filled with a protonfree susceptibility-matching fluid 3 M Corp., St. Paul, MN). Three custom-built, 14 mm diameter solenoid coils with a length of 18.3 mm and over wound ends were used to image three brains in parallel. Parameters used in the scans were optimized for gray/white matter contrast: a T2-weighted, 3D fast spin-echo sequence, with TR/TE ¼ 325/32 msec, four averages, field-of-view 14 mm  14 mm  25 mm and matrix size ¼ 432  432  780 giving an image with 32 mm isotropic voxels. Total imaging time was 11.3 hr . Image Processing The 32 mm isotropic resolution T2-weighted MRI scans were nonlinearly aligned to a three dimensional atlas of the mouse brain with 62 structures identified The end result was that all 12 scans were deformed into exact alignment with each other in an unbiased fashion. This allowed for the analysis of the deformations needed to take each mouse's anatomy into this final atlas space, the goal being to model how the deformation fields relate to genotype. Correspondence with the 3D atlas was obtained by nonlinear alignment of the final stage average MRI with the 40-mouse average MRI upon which the atlas is based MRI Analysis Local differences in brain shape related to genotype were assessed by analysis of the deformation fields Neurochemical Analysis Brain regions were dissected from embryonic or adult Magel2-null or wild-type littermate control mice, snap frozen on dry ice, then stored at À80 C. Brain samples were processed for HPLC combined with fluorescence detection to measure levels of biogenic amines (noradrenaline (NA), dihydroxyphenylacetic acid (DOPAC), dopamine (DA), 5-hydroxyindoleacetic acid (5-HIAA), homovanillic acid (HVA), serotonin (5-HT) and amino acids (Trp, Asp, Glu, Asn, Ser, Gln, Gly, Taur, Ala, GABA)) as described Behavioral Analysis Male Magel2-null mice and their control littermates were tested in the following order at the Centre for Modeling Human Disease: modified SHIRPA for general health, appearance, and neurological reflexes The contextual and cued fear conditioning test was performed using the Video Fear Conditioning system (Med Associates, St. Albans, VT) essentially as described The custom apparatus for the beam test is made up of two platforms (25 cm  35 cm) that are connected with a 90 cm long round beam (18 mm diameter) suspended 50 cm above the floor. One platform was brightly illuminated while the opposite platform MERCER ET AL. 1087 was dark and contained a box providing an enclosed safety area for the mouse. Four consecutive training trials to assist the mouse in navigating the beam were performed on the first day. On the second day, a single trial that recorded the latency to traverse the beam and the number of times the hind feet slipped off was performed. The one-trial object recognition task Behavioral data were analyzed statistically by t-test except the horizontal and vertical activity profile, the 3-day Rotarod test, and the fear-conditioning test, which were analyzed by two-way ANOVA with Bonferroni post-tests, using GraphPad Prism. Probabilities <0.05 were deemed significant. RESULTS Expression of Magel2 in the Adult Mouse Brain We previously outlined expression of Magel2 in the embryonic brain by RNA in situ hybridization General Behavior and Health of Magel2-Null Mice No overt differences in the acquisition of developmental milestones (e.g., physical development, rooting reflex, righting reflex, forelimb/hind limb grasping, or locomotor behavior Neuroanatomical Abnormalities in Magel2-Null Mice Measured by MRI No gross abnormalities in sections of the Magel2-null mouse brains were detected by Nissl staining (not shown). To examine the brain more finely and without the confounding effect of removal from the skull, very high resolution MRI combined with computer analysis was performed. MRI analysis revealed reduced brain volume in the mutant mice (3.4% smaller than control brain, P < 0.01). We used a statistical map of the Jacobian determinant that illustrates the expansion and contraction of tissue based on genotype, to find regions of significant change. In order to account for an inflated amount of false positive findings due to the number of statistical tests employed, the FDR technique was applied The reduced concentration of serotonin or dopamine could be caused by a reduction in the number of dopaminergic or serotonergic neurons in the Magel2-null mouse brains. To examine this possibility, we first examined the location and number of dopaminergic neurons (immunoreactive with an antibody against TH and visualized by confocal microscopy) in the hypothalamus in adult and Magel2-null male mouse brain sections. We found a comparable number of positively staining neurons in both genotypes, and no differences in the appearance of the TH-positive neurons groups in the pre-optic region, the medial basal region, or the medial dorsal region of the hypothalamus (A11-A15 dopaminergic cell groups, Suppl. AMERICAN JOURNAL OF MEDICAL GENETICS PART B with an anti-5-HT antibody revealed no differences in the location or number of serotonergic neurons in the cell groups in the brain stem (Suppl. Magel2-Null Tests of Anxiety and Learning The elevated plus maze is a more specific test of anxiety in a novel environment. The time spent in the open or closed arms, time spent on the end of the open arms and on the central platform, time spent freezing in the open and freezing in the center, the number of passes between closed arms, the number of risk assessments, and the number of head dips were all measured, but no significant differences between genotypes were detected (data not shown). We then used a Pavlovian fear-conditioning test that measures percent of time spent with total lack of movement (freezing) after an aversive stimulus, and the learning associated with this stimulus. This test also models anticipatory anxiety, and requires a combination of amygdalar and hippocampal function. Each mouse was acclimatized in a test context, then a 30 sec auditory tone was used as the conditioned stimulus paired with an aversive unconditioned stimulus, in this case a 2 sec mild foot shock at the end of the tone. After conditioning, either the test context or the tone typically elicit a state of fear even in the absence of the foot shock, in a normal mouse. This fear is manifested as freezing, and is used to measure learning when assessed after 24 hr. The Magel2-null mice tended towards an increased amount of time spent freezing during the baseline measurement on Day 1 (1.2 AE 0.7% for control mice, 12.4 AE 5.7% for the Magel2-null mice, P < 0.09, all values expressed as mean AE standard error of the mean (SEM), Magel2-Null Mice Display Altered Behavior in Novel Environments As a further test to discriminate anxiety from learning, we performed a set of tests that measure reactions to novel objects in an independent cohort of male and female mice that were na€ ıve to behavioral testing. In a one-trial object recognition task, each Latency to fall from an accelerating Rotarod during a single test is significantly increased in the Magel2-null mice; **P < 0.05. E: Latency to fall from an accelerating Rotarod increases for both genotypes over three consecutive days indicating normal motor learning. Latency to fall is significantly increased in the Magel2-null mice (two-way ANOVA, main effect of genotype P < 0.0006). AMERICAN JOURNAL OF MEDICAL GENETICS PART B FIG. 3. Fear conditioning test and novel object scenarios reveal abnormal behavior in Magel2-null mice. A: Magel2-null mice freeze more than wildtype (WT) control mice in the test context at baseline and after the auditory tone, but have similar freezing rates after the foot shock. On Day 2, freezing in the familiar test context was not different between genotypes, but in contrast, Magel2-null mice freeze more than control at baseline in the altered context, pre-tone. Also on Day 2, the net amount of freezing in the novel context either before (pre-tone) or after (tone) the auditory tone was not different between genotypes. Data are expressed as mean AE SEM. Two-way ANOVA detected a main effect of genotype across the six freezing measurements (P < 0.0001). The fold change (x) in freezing during fear conditioning is also presented as a ratio of the means. Fold changes in the test context (tone, shock, day 2 context) are compared to baseline. Fold changes in the altered context after the tone are compared to the pre-tone measurement. Magel2-null mice show a blunted fear reaction to either the test context or to the tone. B: Female Magel2-null display increased exploratory behavior when placed in a cage with two novel objects, with decreased latency to reach 38 sec total exploration time. Data are expressed as mean AE SEM, **P < 0.05. C: Control mice of both sexes and male Magel2-null mice spend more time with the novel object than with the familiar object, measured after 5 min and after 24 hr, and presented as a discrimination index (the difference between the time with the novel object and the time with familiar object divided by the total time). Magel2-null female mice show no preference for a novel object after 3 min (DI ¼ 0, **P < 0.05). D: Male mice of both genotypes buried similar numbers of marbles over the three min. test interval. In contrast, female Magel2-null mice buried significantly fewer marbles than controls; **P < 0.05. E: Control mice consume slightly less food during their first to days in an Accuscan chamber with powdered food, but increase food consumption to normal levels by day 3 in the chamber. In contrast, Magel2-null mice have substantially reduced food intake when initially placed in the Accuscan chamber, and never attain normal levels of food intake. MERCER ET AL. 1093 mouse was removed from the home cage and acclimatized to the test cage in which two objects (e.g., plastic 15 ml tube, 10 ml syringe) were placed. The total length of time needed to accumulate 38 sec of active object exploration was recorded. Magel2-null female mice explored the objects more actively than their control littermates, accumulating 38 sec of exploration time within 141 AE 26 sec, while the control female mice required twice as long to accumulate the total exploration time (321 AE 53 sec, P < 0.02) Wild-type mice typically spend 70% of their time with the novel object and 30% with the familiar object under this paradigm Our hypothesis that Magel2-null mice tend to avoid novel objects and are anxious in novel environments is supported by observations we made during a previous feeding study. In this experiment, male mice were placed in a chamber with a powdered standard chow dispenser that measured hourly food consumption over 5 days Additional Tests of Behavior Mice normally exhibit self-grooming behavior, and pathological self-grooming or excessive grooming of cage mates has been interpreted as evidence of obsessive-compulsive tendencies in mice DISCUSSION Magel2 belongs to the MAGE family of proteins, and is most closely related to MAGED1/NRAGE and necdin. Studies in cell culture and in mice have implicated necdin in neural differentiation and cell cycle exit, and structural and function deficits in the nervous system have been identified in necdin-null mice Magel2-Null Mice Have Reduced Brain Volume and Reduced Neurotransmitter Levels in Discrete Regions of the Brain Subtle changes in regional brain volume have been described in a variety of congenital and progressive genetic disorders, most 1094 AMERICAN JOURNAL OF MEDICAL GENETICS PART B prominently in human and mouse studies of schizophrenia It is difficult to establish a cause and effect relationship between neurochemical imbalances and behavior in mice, particularly as total levels combine the intracellular and extracellular pools of the neurotransmitters. For example, many studies implicating serotonin in mood and behavior use surrogate markers, such as 5-HT or 5-HIAA levels in cerebrospinal fluid or platelets, examine the activation of serotonin receptors after pharmacological intervention, or the effects of depletion of the serotonin precursor tryptophan on behavior. Nonetheless, many studies have linked altered serotonergic and dopaminergic pathways with psychiatric disorders, most notably depression, anxiety, and self-injurious or obsessive behavior Magel2-Null Mice Are Hypoactive and React Abnormally to Novel Environments We performed assays in Magel2-null mice designed to measure anxiety-like behavior, locomotion, balance, neuromuscular function, learning, and memory. Behavioral tests in animal models can provide surrogate markers for normal or pathological human behavior. In transgenic animal studies, interacting deficits in different processes can influence performance in behavior tests Balance and strength were not impaired by the Magel2 mutation, as evidenced by normal or improved function in rearing in the open field, time to cross in the beam test, increased latency to fall from the Rotarod, and equivalent time spent struggling in the tail suspension test. One interpretation of the increased latency to fall from the Rotarod is that the Magel2-null mice have normal strength and balance, as supported by the other tests of motor function, but have increased motivation not to fall, consistent with their abnormal reaction to other novel environments. We did however observe a significant reduction in open field activity in Magel2-null mice, consistent with previous findings that used running wheels to monitor 24 hr activity of Magel2-null mice MERCER ET AL. 1095 We found no evidence for learning or long-term memory deficiencies in the 3-day Rotarod test, the 24 hr novel object preference test, or the 24 hr fear-conditioning test. There was an increase in freezing in the Magel2-null mice on day 2 of the fear conditioning test, suggesting they are not grossly impaired in amygdalar or hippocampal functions required for conditioned learning over 24 hr. The interpretation of learning in the fearconditioning test was complicated by the high baseline freezing rates in the Magel2-null mice, which led to a smaller fold increase in freezing either to the context or to the tone on Day 2. The conditioned fear test revealed a significant difference between genotypes not related to learning or memory: male Magel2-null mice have increased time spent freezing under baseline conditions, indicating increased anxiety in the test chamber. It is unlikely that reduced activity accounts for this increase in freezing during the 2 min baseline measurement, as there was only minimal difference in horizontal or vertical activity between genotypes in the first 5 min of the open field test. Rather, there was a progressive decline in activity of the Magel2-null mice over the following 25 min in the open field. In a test used as a proxy for anxiety in rodents, we found no inter-genotype difference in marble burying activity in male mice, nor was there any difference in the time male mice spent with objects in the cage. In contrast, female Magel2-null mice spent more time exploring objects placed in a cage, did not display novel object preference when placed back into the test chamber after a 5 min interval, and were less likely to bury marbles placed on the surface of the bedding. In summary, the object-based tests with the female mice suggest a combination of poor short-term memory for novel objects and decreased motivation to manipulate objects in the cage. Interestingly, sex-specific differences in behavioral responses to novel objects were also observed in a serotonin-depletion mouse model of developmental brain disorders Abnormalities of Brain and Behavior: Comparison With PWS In PWS, psychiatric symptoms often develop during childhood and can include mood instability, obsessive-compulsive disorder, autism spectrum disorder, cognitive rigidity, anxiety, and addictive behavior towards to food and other substances Although the extrapolation of murine studies to human behavior must be approached with caution, studies of genetically engineered mice have successfully recapitulated the fundamental behavioral aspects of the respective human genetic disorder in many cases Almost all individuals with PWS lack expression of multiple genes, including loss of function of MAGEL2 and necdin, and most PWS candidate genes are moderately to highly expressed in the brain . It is unclear how much contribution to the PWS phenotype is made by each of the deleted genes. Comparison with other mouse strains carrying individual PWS gene deletions may be informative, although few behavioral studies have been performed to date. We previously showed that mice lacking necdin are underweight at birth A report of a child with atypical PWS carrying a chromosome deletion of 175 kb AMERICAN JOURNAL OF MEDICAL GENETICS PART B RNAs (HBII-85) (e.g., ACKNOWLEDGMENT

Dosage-Dependent Phenotypes in Models of Human 16p11.2 Lesions Found in Autism

Recurrent copy number variations (CNVs) of human 16p11.2 have been associated with a variety of developmental/neurocognitive syndromes. In particular, deletion of 16p11.2 is found in patients with autism, developmental delay, and obesity. Patients with deletions or duplications have a wide range of clinical features, and siblings carrying the same deletion often have diverse symptoms. To study the consequence of 16p11.2 CNVs in a systematic manner, we used chromosome engineering to generate mice harboring deletion of the chromosomal region corresponding to 16p11.2, as well as mice harboring the reciprocal duplication. These 16p11.2 CNV models have dosage-dependent changes in gene expression, viability, brain architecture, and behavior. For each phenotype, the consequence of the deletion is more severe than that of the duplication. Of particular note is that half of the 16p11.2 deletion mice die postnatally; those that survive to adulthood are healthy and fertile, but have alterations in the hypothalamus and exhibit a “behavior trap” phenotype—a specific behavior characteristic of rodents with lateral hypothalamic and nigrostriatal lesions. These findings indicate that 16p11.2 CNVs cause brain and behavioral anomalies, providing insight into human neurodevelopmental disorders

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.Comment: 19 page

Human impact on the hydroenvironment of Lake Parishan, SW Iran, through the late Holocene

A multiproxy record from Lake Parishan, SW Iran, shows human impact on the lake and its catchment over the last 4000 years. The Parishan record provides evidence of changes in lake hydrology, from ostracod, diatom and isotope analyses, that are directly linked to human activity in the catchment; recorded by pollen and charcoal and supported by regional archaeological and historical data. The lake ostracod fauna is particularly sensitive to human induced catchment alterations and allow us to identify changes in catchment hydrology that are due to more than a simple change in precipitation: evaporation state. Oxygen isotope data from endogenic carbonates follow these faunal changes but also displays a longer trend to more positive values through the period, coincident with regional patterns of water balance for the late Holocene in the eastern Mediterranean

Effect of molecular and electronic structure on the light harvesting properties of dye sensitizers

The systematic trends in structural and electronic properties of perylene diimide (PDI) derived dye molecules have been investigated by DFT calculations based on projector augmented wave (PAW) method including gradient corrected exchange-correlation effects. TDDFT calculations have been performed to study the visible absorbance activity of these complexes. The effect of different ligands and halogen atoms attached to PDI were studied to characterize the light harvesting properties. The atomic size and electronegativity of the halogen were observed to alter the relaxed molecular geometries which in turn influenced the electronic behavior of the dye molecules. Ground state molecular structure of isolated dye molecules studied in this work depends on both the halogen atom and the carboxylic acid groups. DFT calculations revealed that the carboxylic acid ligands did not play an important role in changing the HOMO-LUMO gap of the sensitizer. However, they serve as anchor between the PDI and substrate titania surface of the solar cell or photocatalyst. A commercially available dye-sensitizer, ruthenium bipyridine (RuBpy), was also studied for electronic and structural properties in order to make a comparison with PDI derivatives for light harvesting properties. Results of this work suggest that fluorinated, chlorinated, brominated, and iyodinated PDI compounds can be useful as sensitizers in solar cells and in artificial photosynthesis.Comment: Single pdf file, 14 pages with 7 figures and 4 table